diff --git a/paddle/framework/prune.cc b/paddle/framework/prune.cc
index 00fe551e55..ddd6b993d4 100644
--- a/paddle/framework/prune.cc
+++ b/paddle/framework/prune.cc
@@ -182,6 +182,7 @@ void prune_impl(const proto::ProgramDesc& input, proto::ProgramDesc* output,
 // TODO(fengjiayi): Prune() could be inplaced to avoid unnecessary copies
 void Prune(const proto::ProgramDesc& input, proto::ProgramDesc* output) {
   std::set<std::string> dependent_vars;
+  output->clear_blocks();
   prune_impl(input, output, 0, -1, dependent_vars);
 }