diff --git a/astrbot/core/provider/sources/gemini_source.py b/astrbot/core/provider/sources/gemini_source.py
index f38fcfc359..5d144f6fdc 100644
--- a/astrbot/core/provider/sources/gemini_source.py
+++ b/astrbot/core/provider/sources/gemini_source.py
@@ -292,6 +292,15 @@ async def _prepare_query_config(
                 else:
                     thinking_config.thinking_level = level
 
+        # If any tools (native or custom function declarations) are active for this request,
+        # we must disable thinking because Gemini API does not support them simultaneously.
+        if tool_list and thinking_config:
+            if getattr(thinking_config, "thinking_budget", None) != 0:
+                logger.warning(
+                    "[Gemini] Thinking config is automatically disabled because tools are active for this request."
+                )
+            thinking_config = None
+
         return types.GenerateContentConfig(
             system_instruction=system_instruction,
             temperature=temperature,
@@ -379,11 +388,10 @@ def append_or_extend(
                 append_or_extend(gemini_contents, parts, types.UserContent)
 
             elif role == "assistant":
-                if isinstance(content, str):
-                    parts = [types.Part.from_text(text=content)]
-                    append_or_extend(gemini_contents, parts, types.ModelContent)
+                parts = []
+                if isinstance(content, str) and content:
+                    parts.append(types.Part.from_text(text=content))
                 elif isinstance(content, list):
-                    parts = []
                     thinking_signature = None
                     text = ""
                     for part in content:
@@ -408,10 +416,8 @@ def append_or_extend(
                             thought_signature=thinking_signature,
                         )
                     )
-                    append_or_extend(gemini_contents, parts, types.ModelContent)
 
-                elif not native_tool_enabled and "tool_calls" in message:
-                    parts = []
+                if not native_tool_enabled and "tool_calls" in message:
                     for tool in message["tool_calls"]:
                         part = types.Part.from_function_call(
                             name=tool["function"]["name"],
@@ -429,15 +435,16 @@ def append_or_extend(
                             if ts_bs64:
                                 part.thought_signature = base64.b64decode(ts_bs64)
                         parts.append(part)
-                    append_or_extend(gemini_contents, parts, types.ModelContent)
-                else:
+
+                if not parts:
                     logger.warning("assistant 角色的消息内容为空，已添加空格占位")
                     if native_tool_enabled and "tool_calls" in message:
                         logger.warning(
                             "检测到启用Gemini原生工具，且上下文中存在函数调用，建议使用 /reset 重置上下文",
                         )
                     parts = [types.Part.from_text(text=" ")]
-                    append_or_extend(gemini_contents, parts, types.ModelContent)
+
+                append_or_extend(gemini_contents, parts, types.ModelContent)
 
             elif role == "tool" and not native_tool_enabled:
                 func_name = message.get("name", message["tool_call_id"])