diff --git a/lightrag/operate.py b/lightrag/operate.py
index 909d55a8..d978d77a 100644
--- a/lightrag/operate.py
+++ b/lightrag/operate.py
@@ -429,8 +429,12 @@ async def _rebuild_knowledge_from_chunks(
         async with semaphore:
             workspace = global_config.get("workspace", "")
             namespace = f"{workspace}:GraphDB" if workspace else "GraphDB"
+            # Sort src and tgt to ensure order-independent lock key generation
+            sorted_key_parts = sorted([src, tgt])
             async with get_storage_keyed_lock(
-                f"{src}-{tgt}", namespace=namespace, enable_logging=False
+                f"{sorted_key_parts[0]}-{sorted_key_parts[1]}",
+                namespace=namespace,
+                enable_logging=False,
             ):
                 try:
                     await _rebuild_single_relationship(