diff --git a/cmake/coveralls.cmake b/cmake/coveralls.cmake
index aad02d24be15535d65f4ac0d0db58fa3cd85c3bf..36a56044fbfcfb2b6572dd4aef58b80bedfb185d 100644
--- a/cmake/coveralls.cmake
+++ b/cmake/coveralls.cmake
@@ -62,7 +62,15 @@ function(code_coverage _COVERAGE_SRCS _COVERALLS_UPLOAD _CMAKE_SCRIPT_PATH)
 endfunction()
 
 if(WITH_COVERAGE)
-    if (NOT ("$ENV{PADDLE_GIT_DIFF_H_FILE}" STREQUAL ""))
+    if (WITH_INCREMENTAL_COVERAGE)
+        # if *.h changed, generate coverage report totaly.
+        # if pybind.cc changed, generate coverage report totaly.
+        # Because if pybind.cc add '-g -O0 -fprofile-arcs -ftest-coverage' only, some testcase will fail.
+        if ( (NOT ("$ENV{PADDLE_GIT_DIFF_H_FILE}" STREQUAL "")) OR ("$ENV{PADDLE_GIT_DIFF_CC_FILE}" MATCHES "pybind.cc") )
+            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0 -fprofile-arcs -ftest-coverage")
+            set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0 -fprofile-arcs -ftest-coverage")
+        endif()
+    else()
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0 -fprofile-arcs -ftest-coverage")
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0 -fprofile-arcs -ftest-coverage")
     endif()
diff --git a/cmake/generic.cmake b/cmake/generic.cmake
index 51cbc534e46a3423f0c4f3f51c5dd25d08b42644..8e1e2f460f4960ec8d4265a06cd57b5aa43017d8 100644
--- a/cmake/generic.cmake
+++ b/cmake/generic.cmake
@@ -267,8 +267,9 @@ function(merge_static_libs TARGET_NAME)
 endfunction(merge_static_libs)
 
 function(check_coverage_opt TARGET_NAME SRCS)
-  if(WITH_COVERAGE)
-    if ("$ENV{PADDLE_GIT_DIFF_H_FILE}" STREQUAL "")
+  if(WITH_COVERAGE AND WITH_INCREMENTAL_COVERAGE)
+    # if pybind.cc add '-g -O0 -fprofile-arcs -ftest-coverage' only, some testcase will fail.
+    if ("$ENV{PADDLE_GIT_DIFF_H_FILE}" STREQUAL "" AND (NOT ("$ENV{PADDLE_GIT_DIFF_CC_FILE}" MATCHES "pybind.cc")))
       if (NOT ("$ENV{PADDLE_GIT_DIFF_CC_FILE}" STREQUAL ""))
         string(REPLACE "," ";" CC_FILE_LIST $ENV{PADDLE_GIT_DIFF_CC_FILE})
         set(use_coverage_opt FALSE)