diff --git a/agent/component/agent_with_tools.py b/agent/component/agent_with_tools.py
index 56f23afe350..39052eb425b 100644
--- a/agent/component/agent_with_tools.py
+++ b/agent/component/agent_with_tools.py
@@ -32,7 +32,7 @@
 from api.db.services.mcp_server_service import MCPServerService
 from api.db.services.tenant_llm_service import TenantLLMService
 from common.connection_utils import timeout
-from common.mcp_tool_call_conn import MCPToolCallSession, mcp_tool_metadata_to_openai_tool
+from common.mcp_tool_call_conn import MCPToolBinding, MCPToolCallSession, mcp_tool_metadata_to_openai_tool
 from rag.prompts.generator import citation_plus, citation_prompt, full_question, kb_prompt, message_fit_in, structured_output_prompt
 
 
@@ -97,13 +97,16 @@ def __init__(self, canvas, id, param: LLMParam):
             indexed_meta["function"]["name"] = indexed_name
             self.tool_meta.append(indexed_meta)
 
+        tool_idx = len(self.tools)
         for mcp in self._param.mcp:
             _, mcp_server = MCPServerService.get_by_id(mcp["mcp_id"])
             custom_header = self._param.custom_header
             tool_call_session = MCPToolCallSession(mcp_server, mcp_server.variables, custom_header)
             for tnm, meta in mcp["tools"].items():
-                self.tool_meta.append(mcp_tool_metadata_to_openai_tool(meta))
-                self.tools[tnm] = tool_call_session
+                indexed_name = f"{tnm}_{tool_idx}"
+                tool_idx += 1
+                self.tool_meta.append(mcp_tool_metadata_to_openai_tool(meta, function_name=indexed_name))
+                self.tools[indexed_name] = MCPToolBinding(tool_call_session, tnm)
         self.callback = partial(self._canvas.tool_use_callback, id)
         self.toolcall_session = LLMToolPluginCallSession(self.tools, self.callback)
         if self.tool_meta:
diff --git a/agent/tools/base.py b/agent/tools/base.py
index f5a42de4d10..0110a84142f 100644
--- a/agent/tools/base.py
+++ b/agent/tools/base.py
@@ -23,7 +23,7 @@
 from agent.component.base import ComponentParamBase, ComponentBase
 from common.misc_utils import hash_str2int
 from rag.prompts.generator import kb_prompt
-from common.mcp_tool_call_conn import MCPToolCallSession, ToolCallSession
+from common.mcp_tool_call_conn import MCPToolBinding, MCPToolCallSession, ToolCallSession
 from timeit import default_timer as timer
 
 
@@ -52,16 +52,18 @@ def __init__(self, tools_map: dict[str, object], callback: partial):
         self.tools_map = tools_map
         self.callback = callback
 
-    def tool_call(self, name: str, arguments: dict[str, Any]) -> Any:
-        return asyncio.run(self.tool_call_async(name, arguments))
+    def tool_call(self, name: str, arguments: dict[str, Any], timeout: float | int = 10) -> Any:
+        return asyncio.run(self.tool_call_async(name, arguments, request_timeout=timeout))
 
-    async def tool_call_async(self, name: str, arguments: dict[str, Any]) -> Any:
+    async def tool_call_async(self, name: str, arguments: dict[str, Any], request_timeout: float | int = 10) -> Any:
         assert name in self.tools_map, f"LLM tool {name} does not exist"
         logging.info(f"[ToolCall] invoke name={name} arguments={str(arguments)[:200]}")
         st = timer()
         tool_obj = self.tools_map[name]
-        if isinstance(tool_obj, MCPToolCallSession):
-            resp = await thread_pool_exec(tool_obj.tool_call, name, arguments, 60)
+        if isinstance(tool_obj, MCPToolBinding):
+            resp = await thread_pool_exec(tool_obj.session.tool_call, tool_obj.original_name, arguments, request_timeout)
+        elif isinstance(tool_obj, MCPToolCallSession):
+            resp = await thread_pool_exec(tool_obj.tool_call, name, arguments, request_timeout)
         elif hasattr(tool_obj, "invoke_async") and asyncio.iscoroutinefunction(tool_obj.invoke_async):
             resp = await tool_obj.invoke_async(**arguments)
         else:
diff --git a/common/mcp_tool_call_conn.py b/common/mcp_tool_call_conn.py
index 95e3581bb0b..676978d052e 100644
--- a/common/mcp_tool_call_conn.py
+++ b/common/mcp_tool_call_conn.py
@@ -20,6 +20,7 @@
 import weakref
 from concurrent.futures import ThreadPoolExecutor
 from concurrent.futures import TimeoutError as FuturesTimeoutError
+from dataclasses import dataclass
 from string import Template
 from typing import Any, Literal, Protocol
 
@@ -36,7 +37,13 @@
 
 
 class ToolCallSession(Protocol):
-    def tool_call(self, name: str, arguments: dict[str, Any]) -> str: ...
+    def tool_call(self, name: str, arguments: dict[str, Any], timeout: float | int = 10) -> str: ...
+
+
+@dataclass(frozen=True)
+class MCPToolBinding:
+    session: ToolCallSession
+    original_name: str
 
 
 class MCPToolCallSession(ToolCallSession):
@@ -316,12 +323,12 @@ def shutdown_all_mcp_sessions():
     logging.info("All MCPToolCallSession instances have been closed.")
 
 
-def mcp_tool_metadata_to_openai_tool(mcp_tool: Tool | dict) -> dict[str, Any]:
+def mcp_tool_metadata_to_openai_tool(mcp_tool: Tool | dict, function_name: str | None = None) -> dict[str, Any]:
     if isinstance(mcp_tool, dict):
         return {
             "type": "function",
             "function": {
-                "name": mcp_tool["name"],
+                "name": function_name or mcp_tool["name"],
                 "description": mcp_tool["description"],
                 "parameters": mcp_tool["inputSchema"],
             },
@@ -330,7 +337,7 @@ def mcp_tool_metadata_to_openai_tool(mcp_tool: Tool | dict) -> dict[str, Any]:
     return {
         "type": "function",
         "function": {
-            "name": mcp_tool.name,
+            "name": function_name or mcp_tool.name,
             "description": mcp_tool.description,
             "parameters": mcp_tool.inputSchema,
         },