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ToolsMCP servers with Qwen Code

MCP servers with Qwen Code

This document provides a guide to configuring and using Model Context Protocol (MCP) servers with Qwen Code.

What is an MCP server?

An MCP server is an application that exposes tools and resources to the CLI through the Model Context Protocol, allowing it to interact with external systems and data sources. MCP servers act as a bridge between the model and your local environment or other services like APIs.

An MCP server enables the CLI to:

  • Discover tools: List available tools, their descriptions, and parameters through standardized schema definitions.
  • Execute tools: Call specific tools with defined arguments and receive structured responses.
  • Access resources: Read data from specific resources (though the CLI primarily focuses on tool execution).

With an MCP server, you can extend the CLI’s capabilities to perform actions beyond its built-in features, such as interacting with databases, APIs, custom scripts, or specialized workflows.

Core Integration Architecture

Qwen Code integrates with MCP servers through a sophisticated discovery and execution system built into the core package (packages/core/src/tools/):

Discovery Layer (mcp-client.ts)

The discovery process is orchestrated by discoverMcpTools(), which:

  1. Iterates through configured servers from your settings.json mcpServers configuration
  2. Establishes connections using appropriate transport mechanisms (Stdio, SSE, or Streamable HTTP)
  3. Fetches tool definitions from each server using the MCP protocol
  4. Sanitizes and validates tool schemas for compatibility with the Gemini API
  5. Registers tools in the global tool registry with conflict resolution

Execution Layer (mcp-tool.ts)

Each discovered MCP tool is wrapped in a DiscoveredMCPTool instance that:

  • Handles confirmation logic based on server trust settings and user preferences
  • Manages tool execution by calling the MCP server with proper parameters
  • Processes responses for both the LLM context and user display
  • Maintains connection state and handles timeouts

Transport Mechanisms

The CLI supports three MCP transport types:

  • Stdio Transport: Spawns a subprocess and communicates via stdin/stdout
  • SSE Transport: Connects to Server-Sent Events endpoints
  • Streamable HTTP Transport: Uses HTTP streaming for communication

How to set up your MCP server

Qwen Code uses the mcpServers configuration in your settings.json file to locate and connect to MCP servers. This configuration supports multiple servers with different transport mechanisms.

Configure the MCP server in settings.json

You can configure MCP servers at the global level in the ~/.qwen/settings.json file or in your project’s root directory, create or open the .qwen/settings.json file. Within the file, add the mcpServers configuration block.

Configuration Structure

Add an mcpServers object to your settings.json file:

{ ...file contains other config objects
  "mcpServers": {
    "serverName": {
      "command": "path/to/server",
      "args": ["--arg1", "value1"],
      "env": {
        "API_KEY": "$MY_API_TOKEN"
      },
      "cwd": "./server-directory",
      "timeout": 30000,
      "trust": false
    }
  }
}

Configuration Properties

Each server configuration supports the following properties:

Required (one of the following)

  • command (string): Path to the executable for Stdio transport
  • url (string): SSE endpoint URL (e.g., "http://localhost:8080/sse")
  • httpUrl (string): HTTP streaming endpoint URL

Optional

  • args (string[]): Command-line arguments for Stdio transport
  • headers (object): Custom HTTP headers when using url or httpUrl
  • env (object): Environment variables for the server process. Values can reference environment variables using $VAR_NAME or ${VAR_NAME} syntax
  • cwd (string): Working directory for Stdio transport
  • timeout (number): Request timeout in milliseconds (default: 600,000ms = 10 minutes)
  • trust (boolean): When true, bypasses all tool call confirmations for this server (default: false)
  • includeTools (string[]): List of tool names to include from this MCP server. When specified, only the tools listed here will be available from this server (whitelist behavior). If not specified, all tools from the server are enabled by default.
  • excludeTools (string[]): List of tool names to exclude from this MCP server. Tools listed here will not be available to the model, even if they are exposed by the server. Note: excludeTools takes precedence over includeTools - if a tool is in both lists, it will be excluded.

OAuth Support for Remote MCP Servers

Qwen Code supports OAuth 2.0 authentication for remote MCP servers using SSE or HTTP transports. This enables secure access to MCP servers that require authentication.

Automatic OAuth Discovery

For servers that support OAuth discovery, you can omit the OAuth configuration and let the CLI discover it automatically:

{
  "mcpServers": {
    "discoveredServer": {
      "url": "https://api.example.com/sse"
    }
  }
}

The CLI will automatically:

  • Detect when a server requires OAuth authentication (401 responses)
  • Discover OAuth endpoints from server metadata
  • Perform dynamic client registration if supported
  • Handle the OAuth flow and token management

Authentication Flow

When connecting to an OAuth-enabled server:

  1. Initial connection attempt fails with 401 Unauthorized
  2. OAuth discovery finds authorization and token endpoints
  3. Browser opens for user authentication (requires local browser access)
  4. Authorization code is exchanged for access tokens
  5. Tokens are stored securely for future use
  6. Connection retry succeeds with valid tokens

Browser Redirect Requirements

Important: OAuth authentication requires that your local machine can:

  • Open a web browser for authentication
  • Receive redirects on http://localhost:7777/oauth/callback

This feature will not work in:

  • Headless environments without browser access
  • Remote SSH sessions without X11 forwarding
  • Containerized environments without browser support

Managing OAuth Authentication

Use the /mcp auth command to manage OAuth authentication:

# List servers requiring authentication
/mcp auth
 
# Authenticate with a specific server
/mcp auth serverName
 
# Re-authenticate if tokens expire
/mcp auth serverName

OAuth Configuration Properties

  • enabled (boolean): Enable OAuth for this server
  • clientId (string): OAuth client identifier (optional with dynamic registration)
  • clientSecret (string): OAuth client secret (optional for public clients)
  • authorizationUrl (string): OAuth authorization endpoint (auto-discovered if omitted)
  • tokenUrl (string): OAuth token endpoint (auto-discovered if omitted)
  • scopes (string[]): Required OAuth scopes
  • redirectUri (string): Custom redirect URI (defaults to http://localhost:7777/oauth/callback)
  • tokenParamName (string): Query parameter name for tokens in SSE URLs
  • audiences (string[]): Audiences the token is valid for

Token Management

OAuth tokens are automatically:

  • Stored securely in ~/.qwen/mcp-oauth-tokens.json
  • Refreshed when expired (if refresh tokens are available)
  • Validated before each connection attempt
  • Cleaned up when invalid or expired

Authentication Provider Type

You can specify the authentication provider type using the authProviderType property:

  • authProviderType (string): Specifies the authentication provider. Can be one of the following:
    • dynamic_discovery (default): The CLI will automatically discover the OAuth configuration from the server.
    • google_credentials: The CLI will use the Google Application Default Credentials (ADC) to authenticate with the server. When using this provider, you must specify the required scopes.
{
  "mcpServers": {
    "googleCloudServer": {
      "httpUrl": "https://my-gcp-service.run.app/mcp",
      "authProviderType": "google_credentials",
      "oauth": {
        "scopes": ["https://www.googleapis.com/auth/userinfo.email"]
      }
    }
  }
}

Example Configurations

Python MCP Server (Stdio)

{
  "mcpServers": {
    "pythonTools": {
      "command": "python",
      "args": ["-m", "my_mcp_server", "--port", "8080"],
      "cwd": "./mcp-servers/python",
      "env": {
        "DATABASE_URL": "$DB_CONNECTION_STRING",
        "API_KEY": "${EXTERNAL_API_KEY}"
      },
      "timeout": 15000
    }
  }
}

Node.js MCP Server (Stdio)

{
  "mcpServers": {
    "nodeServer": {
      "command": "node",
      "args": ["dist/server.js", "--verbose"],
      "cwd": "./mcp-servers/node",
      "trust": true
    }
  }
}

Docker-based MCP Server

{
  "mcpServers": {
    "dockerizedServer": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e",
        "API_KEY",
        "-v",
        "${PWD}:/workspace",
        "my-mcp-server:latest"
      ],
      "env": {
        "API_KEY": "$EXTERNAL_SERVICE_TOKEN"
      }
    }
  }
}

HTTP-based MCP Server

{
  "mcpServers": {
    "httpServer": {
      "httpUrl": "http://localhost:3000/mcp",
      "timeout": 5000
    }
  }
}

HTTP-based MCP Server with Custom Headers

{
  "mcpServers": {
    "httpServerWithAuth": {
      "httpUrl": "http://localhost:3000/mcp",
      "headers": {
        "Authorization": "Bearer your-api-token",
        "X-Custom-Header": "custom-value",
        "Content-Type": "application/json"
      },
      "timeout": 5000
    }
  }
}

MCP Server with Tool Filtering

{
  "mcpServers": {
    "filteredServer": {
      "command": "python",
      "args": ["-m", "my_mcp_server"],
      "includeTools": ["safe_tool", "file_reader", "data_processor"],
      // "excludeTools": ["dangerous_tool", "file_deleter"],
      "timeout": 30000
    }
  }
}

Discovery Process Deep Dive

When Qwen Code starts, it performs MCP server discovery through the following detailed process:

1. Server Iteration and Connection

For each configured server in mcpServers:

  1. Status tracking begins: Server status is set to CONNECTING
  2. Transport selection: Based on configuration properties:
    • httpUrl → StreamableHTTPClientTransport
    • url → SSEClientTransport
    • command → StdioClientTransport
  3. Connection establishment: The MCP client attempts to connect with the configured timeout
  4. Error handling: Connection failures are logged and the server status is set to DISCONNECTED

2. Tool Discovery

Upon successful connection:

  1. Tool listing: The client calls the MCP server’s tool listing endpoint
  2. Schema validation: Each tool’s function declaration is validated
  3. Tool filtering: Tools are filtered based on includeTools and excludeTools configuration
  4. Name sanitization: Tool names are cleaned to meet Gemini API requirements:
    • Invalid characters (non-alphanumeric, underscore, dot, hyphen) are replaced with underscores
    • Names longer than 63 characters are truncated with middle replacement (___)

3. Conflict Resolution

When multiple servers expose tools with the same name:

  1. First registration wins: The first server to register a tool name gets the unprefixed name
  2. Automatic prefixing: Subsequent servers get prefixed names: serverName__toolName
  3. Registry tracking: The tool registry maintains mappings between server names and their tools

4. Schema Processing

Tool parameter schemas undergo sanitization for API compatibility:

  • $schema properties are removed
  • additionalProperties are stripped
  • anyOf with default have their default values removed (Vertex AI compatibility)
  • Recursive processing applies to nested schemas

5. Connection Management

After discovery:

  • Persistent connections: Servers that successfully register tools maintain their connections
  • Cleanup: Servers that provide no usable tools have their connections closed
  • Status updates: Final server statuses are set to CONNECTED or DISCONNECTED

Tool Execution Flow

When the model decides to use an MCP tool, the following execution flow occurs:

1. Tool Invocation

The model generates a FunctionCall with:

  • Tool name: The registered name (potentially prefixed)
  • Arguments: JSON object matching the tool’s parameter schema

2. Confirmation Process

Each DiscoveredMCPTool implements sophisticated confirmation logic:

Trust-based Bypass

if (this.trust) {
  return false; // No confirmation needed
}

Dynamic Allow-listing

The system maintains internal allow-lists for:

  • Server-level: serverName → All tools from this server are trusted
  • Tool-level: serverName.toolName → This specific tool is trusted

User Choice Handling

When confirmation is required, users can choose:

  • Proceed once: Execute this time only
  • Always allow this tool: Add to tool-level allow-list
  • Always allow this server: Add to server-level allow-list
  • Cancel: Abort execution

3. Execution

Upon confirmation (or trust bypass):

  1. Parameter preparation: Arguments are validated against the tool’s schema

  2. MCP call: The underlying CallableTool invokes the server with:

    const functionCalls = [
  {
    name: this.serverToolName, // Original server tool name
    args: params,
  },
];

  3. Response processing: Results are formatted for both LLM context and user display

4. Response Handling

The execution result contains:

  • llmContent: Raw response parts for the language model’s context
  • returnDisplay: Formatted output for user display (often JSON in markdown code blocks)

How to interact with your MCP server

Using the /mcp Command

The /mcp command provides comprehensive information about your MCP server setup:

/mcp

This displays:

  • Server list: All configured MCP servers
  • Connection status: CONNECTED, CONNECTING, or DISCONNECTED
  • Server details: Configuration summary (excluding sensitive data)
  • Available tools: List of tools from each server with descriptions
  • Discovery state: Overall discovery process status

Example /mcp Output

MCP Servers Status:

📡 pythonTools (CONNECTED)
  Command: python -m my_mcp_server --port 8080
  Working Directory: ./mcp-servers/python
  Timeout: 15000ms
  Tools: calculate_sum, file_analyzer, data_processor

🔌 nodeServer (DISCONNECTED)
  Command: node dist/server.js --verbose
  Error: Connection refused

🐳 dockerizedServer (CONNECTED)
  Command: docker run -i --rm -e API_KEY my-mcp-server:latest
  Tools: docker__deploy, docker__status

Discovery State: COMPLETED

Tool Usage

Once discovered, MCP tools are available to the Gemini model like built-in tools. The model will automatically:

  1. Select appropriate tools based on your requests
  2. Present confirmation dialogs (unless the server is trusted)
  3. Execute tools with proper parameters
  4. Display results in a user-friendly format

Status Monitoring and Troubleshooting

Connection States

The MCP integration tracks several states:

Server Status (MCPServerStatus)

  • DISCONNECTED: Server is not connected or has errors
  • CONNECTING: Connection attempt in progress
  • CONNECTED: Server is connected and ready

Discovery State (MCPDiscoveryState)

  • NOT_STARTED: Discovery hasn’t begun
  • IN_PROGRESS: Currently discovering servers
  • COMPLETED: Discovery finished (with or without errors)

Common Issues and Solutions

Server Won’t Connect

Symptoms: Server shows DISCONNECTED status

Troubleshooting:

  1. Check configuration: Verify command, args, and cwd are correct
  2. Test manually: Run the server command directly to ensure it works
  3. Check dependencies: Ensure all required packages are installed
  4. Review logs: Look for error messages in the CLI output
  5. Verify permissions: Ensure the CLI can execute the server command

No Tools Discovered

Symptoms: Server connects but no tools are available

Troubleshooting:

  1. Verify tool registration: Ensure your server actually registers tools
  2. Check MCP protocol: Confirm your server implements the MCP tool listing correctly
  3. Review server logs: Check stderr output for server-side errors
  4. Test tool listing: Manually test your server’s tool discovery endpoint

Tools Not Executing

Symptoms: Tools are discovered but fail during execution

Troubleshooting:

  1. Parameter validation: Ensure your tool accepts the expected parameters
  2. Schema compatibility: Verify your input schemas are valid JSON Schema
  3. Error handling: Check if your tool is throwing unhandled exceptions
  4. Timeout issues: Consider increasing the timeout setting

Sandbox Compatibility

Symptoms: MCP servers fail when sandboxing is enabled

Solutions:

  1. Docker-based servers: Use Docker containers that include all dependencies
  2. Path accessibility: Ensure server executables are available in the sandbox
  3. Network access: Configure sandbox to allow necessary network connections
  4. Environment variables: Verify required environment variables are passed through

Debugging Tips

  1. Enable debug mode: Run the CLI with --debug for verbose output
  2. Check stderr: MCP server stderr is captured and logged (INFO messages filtered)
  3. Test isolation: Test your MCP server independently before integrating
  4. Incremental setup: Start with simple tools before adding complex functionality
  5. Use /mcp frequently: Monitor server status during development

Important Notes

Security Considerations

  • Trust settings: The trust option bypasses all confirmation dialogs. Use cautiously and only for servers you completely control
  • Access tokens: Be security-aware when configuring environment variables containing API keys or tokens
  • Sandbox compatibility: When using sandboxing, ensure MCP servers are available within the sandbox environment
  • Private data: Using broadly scoped personal access tokens can lead to information leakage between repositories

Performance and Resource Management

  • Connection persistence: The CLI maintains persistent connections to servers that successfully register tools
  • Automatic cleanup: Connections to servers providing no tools are automatically closed
  • Timeout management: Configure appropriate timeouts based on your server’s response characteristics
  • Resource monitoring: MCP servers run as separate processes and consume system resources

Schema Compatibility

  • Property stripping: The system automatically removes certain schema properties ($schema, additionalProperties) for Gemini API compatibility
  • Name sanitization: Tool names are automatically sanitized to meet API requirements
  • Conflict resolution: Tool name conflicts between servers are resolved through automatic prefixing

This comprehensive integration makes MCP servers a powerful way to extend the CLI’s capabilities while maintaining security, reliability, and ease of use.

Returning Rich Content from Tools

MCP tools are not limited to returning simple text. You can return rich, multi-part content, including text, images, audio, and other binary data in a single tool response. This allows you to build powerful tools that can provide diverse information to the model in a single turn.

All data returned from the tool is processed and sent to the model as context for its next generation, enabling it to reason about or summarize the provided information.

How It Works

To return rich content, your tool’s response must adhere to the MCP specification for a CallToolResult. The content field of the result should be an array of ContentBlock objects. The CLI will correctly process this array, separating text from binary data and packaging it for the model.

You can mix and match different content block types in the content array. The supported block types include:

  • text
  • image
  • audio
  • resource (embedded content)
  • resource_link

Example: Returning Text and an Image

Here is an example of a valid JSON response from an MCP tool that returns both a text description and an image:

{
  "content": [
    {
      "type": "text",
      "text": "Here is the logo you requested."
    },
    {
      "type": "image",
      "data": "BASE64_ENCODED_IMAGE_DATA_HERE",
      "mimeType": "image/png"
    },
    {
      "type": "text",
      "text": "The logo was created in 2025."
    }
  ]
}

When Qwen Code receives this response, it will:

  1. Extract all the text and combine it into a single functionResponse part for the model.
  2. Present the image data as a separate inlineData part.
  3. Provide a clean, user-friendly summary in the CLI, indicating that both text and an image were received.

This enables you to build sophisticated tools that can provide rich, multi-modal context to the Gemini model.

MCP Prompts as Slash Commands

In addition to tools, MCP servers can expose predefined prompts that can be executed as slash commands within Qwen Code. This allows you to create shortcuts for common or complex queries that can be easily invoked by name.

Defining Prompts on the Server

Here’s a small example of a stdio MCP server that defines prompts:

import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
import { z } from 'zod';
 
const server = new McpServer({
  name: 'prompt-server',
  version: '1.0.0',
});
 
server.registerPrompt(
  'poem-writer',
  {
    title: 'Poem Writer',
    description: 'Write a nice haiku',
    argsSchema: { title: z.string(), mood: z.string().optional() },
  },
  ({ title, mood }) => ({
    messages: [
      {
        role: 'user',
        content: {
          type: 'text',
          text: `Write a haiku${mood ? ` with the mood ${mood}` : ''} called ${title}. Note that a haiku is 5 syllables followed by 7 syllables followed by 5 syllables `,
        },
      },
    ],
  }),
);
 
const transport = new StdioServerTransport();
await server.connect(transport);

This can be included in settings.json under mcpServers with:

"nodeServer": {
  "command": "node",
  "args": ["filename.ts"],
}

Invoking Prompts

Once a prompt is discovered, you can invoke it using its name as a slash command. The CLI will automatically handle parsing arguments.

/poem-writer --title="Qwen Code" --mood="reverent"

or, using positional arguments:

/poem-writer "Qwen Code" reverent

When you run this command, the CLI executes the prompts/get method on the MCP server with the provided arguments. The server is responsible for substituting the arguments into the prompt template and returning the final prompt text. The CLI then sends this prompt to the model for execution. This provides a convenient way to automate and share common workflows.

Managing MCP Servers with qwen mcp

While you can always configure MCP servers by manually editing your settings.json file, the CLI provides a convenient set of commands to manage your server configurations programmatically. These commands streamline the process of adding, listing, and removing MCP servers without needing to directly edit JSON files.

Adding a Server (qwen mcp add)

The add command configures a new MCP server in your settings.json. Based on the scope (-s, --scope), it will be added to either the user config ~/.qwen/settings.json or the project config .qwen/settings.json file.

Command:

qwen mcp add [options] <name> <commandOrUrl> [args...]
  • <name>: A unique name for the server.
  • <commandOrUrl>: The command to execute (for stdio) or the URL (for http/sse).
  • [args...]: Optional arguments for a stdio command.

Options (Flags):

  • -s, --scope: Configuration scope (user or project). [default: “project”]
  • -t, --transport: Transport type (stdio, sse, http). [default: “stdio”]
  • -e, --env: Set environment variables (e.g. -e KEY=value).
  • -H, --header: Set HTTP headers for SSE and HTTP transports (e.g. -H “X-Api-Key: abc123” -H “Authorization: Bearer abc123”).
  • --timeout: Set connection timeout in milliseconds.
  • --trust: Trust the server (bypass all tool call confirmation prompts).
  • --description: Set the description for the server.
  • --include-tools: A comma-separated list of tools to include.
  • --exclude-tools: A comma-separated list of tools to exclude.

Adding an stdio server

This is the default transport for running local servers.

# Basic syntax
qwen mcp add <name> <command> [args...]
 
# Example: Adding a local server
qwen mcp add my-stdio-server -e API_KEY=123 /path/to/server arg1 arg2 arg3
 
# Example: Adding a local python server
qwen mcp add python-server python server.py --port 8080

Adding an HTTP server

This transport is for servers that use the streamable HTTP transport.

# Basic syntax
qwen mcp add --transport http <name> <url>
 
# Example: Adding an HTTP server
qwen mcp add --transport http http-server https://api.example.com/mcp/
 
# Example: Adding an HTTP server with an authentication header
qwen mcp add --transport http secure-http https://api.example.com/mcp/ --header "Authorization: Bearer abc123"

Adding an SSE server

This transport is for servers that use Server-Sent Events (SSE).

# Basic syntax
qwen mcp add --transport sse <name> <url>
 
# Example: Adding an SSE server
qwen mcp add --transport sse sse-server https://api.example.com/sse/
 
# Example: Adding an SSE server with an authentication header
qwen mcp add --transport sse secure-sse https://api.example.com/sse/ --header "Authorization: Bearer abc123"

Listing Servers (qwen mcp list)

To view all MCP servers currently configured, use the list command. It displays each server’s name, configuration details, and connection status.

Command:

qwen mcp list

Example Output:

✓ stdio-server: command: python3 server.py (stdio) - Connected
✓ http-server: https://api.example.com/mcp (http) - Connected
✗ sse-server: https://api.example.com/sse (sse) - Disconnected

Removing a Server (qwen mcp remove)

To delete a server from your configuration, use the remove command with the server’s name.

Command:

qwen mcp remove <name>

Example:

qwen mcp remove my-server

This will find and delete the “my-server” entry from the mcpServers object in the appropriate settings.json file based on the scope (-s, --scope).

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