diff --git a/paddle/fluid/framework/details/op_handle_base.h b/paddle/fluid/framework/details/op_handle_base.h
index fe1735d05dde5f09d5c72c68e5002d16f0083eb5..8f94206a87dbae8a81727ca48718886bbabbe25c 100644
--- a/paddle/fluid/framework/details/op_handle_base.h
+++ b/paddle/fluid/framework/details/op_handle_base.h
@@ -70,6 +70,14 @@ class OpHandleBase {
 
   const std::vector<VarHandleBase *> &Inputs() const { return inputs_; }
 
+  size_t NoDupInputSize() const {
+    std::unordered_set<VarHandleBase *> res;
+    for (auto *var : inputs_) {
+      res.emplace(var);
+    }
+    return res.size();
+  }
+
   const std::vector<VarHandleBase *> &Outputs() const { return outputs_; }
 
  protected:
diff --git a/paddle/fluid/framework/details/threaded_ssa_graph_executor.cc b/paddle/fluid/framework/details/threaded_ssa_graph_executor.cc
index ef263d82c5ec93f0673eb0ac70e4fb02904bff13..815f739371e77d953a28be99b38ec1b8ff26506c 100644
--- a/paddle/fluid/framework/details/threaded_ssa_graph_executor.cc
+++ b/paddle/fluid/framework/details/threaded_ssa_graph_executor.cc
@@ -174,7 +174,7 @@ void ThreadedSSAGraphExecutor::InsertFetchOps(
 void ThreadedSSAGraphExecutor::InsertPendingOp(
     std::unordered_map<OpHandleBase *, size_t> *pending_ops,
     OpHandleBase *op_instance) const {
-  pending_ops->insert({op_instance, op_instance->Inputs().size()});
+  pending_ops->insert({op_instance, op_instance->NoDupInputSize()});
 }
 
 void ThreadedSSAGraphExecutor::InsertPendingVar(