diff --git a/cmake/external/protobuf.cmake b/cmake/external/protobuf.cmake
index e05b7694ddf1e1652b00f156cde1a2d433c9fc46..3da3f10d7c91094ff8ae7daeadfb55e4e44eb731 100644
--- a/cmake/external/protobuf.cmake
+++ b/cmake/external/protobuf.cmake
@@ -203,7 +203,7 @@ FUNCTION(build_protobuf TARGET_NAME BUILD_FOR_HOST)
     ENDIF()
 
     SET(PROTOBUF_REPO "https://github.com/google/protobuf.git")
-    SET(PROTOBUF_TAG "9f75c5aa851cd877fb0d93ccc31b8567a6706546")
+    SET(PROTOBUF_TAG "v3.6.1")
 
     ExternalProject_Add(
         ${TARGET_NAME}
@@ -231,7 +231,7 @@ FUNCTION(build_protobuf TARGET_NAME BUILD_FOR_HOST)
     )
 ENDFUNCTION()
 
-SET(PROTOBUF_VERSION 3.1)
+SET(PROTOBUF_VERSION 3.6.1)
 
 IF(NOT PROTOBUF_FOUND)
     build_protobuf(extern_protobuf FALSE)
diff --git a/cmake/external/python.cmake b/cmake/external/python.cmake
index 623c53f4f75bbd217c157bcdda0cb12c510269ee..351e7fa3ce227ee3a92f527fc49c873e52342594 100644
--- a/cmake/external/python.cmake
+++ b/cmake/external/python.cmake
@@ -74,8 +74,8 @@ IF(PYTHONINTERP_FOUND)
     find_python_module(wheel REQUIRED)
     find_python_module(google.protobuf REQUIRED)
     FIND_PACKAGE(NumPy REQUIRED)
-    IF(${PY_GOOGLE.PROTOBUF_VERSION} AND ${PY_GOOGLE.PROTOBUF_VERSION} VERSION_LESS "3.0.0")
-        MESSAGE(FATAL_ERROR "Found Python Protobuf ${PY_GOOGLE.PROTOBUF_VERSION} < 3.0.0, "
+    IF(${PY_GOOGLE.PROTOBUF_VERSION} AND ${PY_GOOGLE.PROTOBUF_VERSION} VERSION_LESS "3.6.1")
+        MESSAGE(FATAL_ERROR "Found Python Protobuf ${PY_GOOGLE.PROTOBUF_VERSION} < 3.6.1, "
         "please use pip to upgrade protobuf. pip install -U protobuf")
     ENDIF()
 ENDIF(PYTHONINTERP_FOUND)
diff --git a/paddle/scripts/paddle_build.sh b/paddle/scripts/paddle_build.sh
index 1135caf4f8c32901d93270d372fdaac702acf006..e7078499cae87b8a255c6c6d4774052e1f768aa7 100755
--- a/paddle/scripts/paddle_build.sh
+++ b/paddle/scripts/paddle_build.sh
@@ -88,6 +88,7 @@ function cmake_gen() {
             -DPYTHON_INCLUDE_DIR:PATH=/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m/
             -DPYTHON_LIBRARY:FILEPATH=/Library/Frameworks/Python.framework/Versions/3.5/lib/libpython3.5m.dylib"
                 WITH_FLUID_ONLY=${WITH_FLUID_ONLY:-ON}
+                pip3.5 uninstall -y protobuf
                 pip3.5 install --user -r ${PADDLE_ROOT}/python/requirements.txt
             else
                 exit 1
@@ -101,6 +102,7 @@ function cmake_gen() {
             -DPYTHON_INCLUDE_DIR:PATH=/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m/
             -DPYTHON_LIBRARY:FILEPATH=/Library/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6m.dylib"
                 WITH_FLUID_ONLY=${WITH_FLUID_ONLY:-ON}
+                pip3.6 uninstall -y protobuf
                 pip3.6 install --user -r ${PADDLE_ROOT}/python/requirements.txt
             else
                 exit 1
@@ -114,6 +116,7 @@ function cmake_gen() {
             -DPYTHON_INCLUDE_DIR:PATH=/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m/
             -DPYTHON_LIBRARY:FILEPATH=/Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib"
                 WITH_FLUID_ONLY=${WITH_FLUID_ONLY:-ON}
+                pip3.7 uninstall -y protobuf
                 pip3.7 install --user -r ${PADDLE_ROOT}/python/requirements.txt
             else
                 exit 1
@@ -128,31 +131,44 @@ function cmake_gen() {
                 PYTHON_FLAGS="-DPYTHON_EXECUTABLE:FILEPATH=/opt/python/cp27-cp27m/bin/python
             -DPYTHON_INCLUDE_DIR:PATH=/opt/python/cp27-cp27m/include/python2.7
             -DPYTHON_LIBRARIES:FILEPATH=/opt/_internal/cpython-2.7.11-ucs2/lib/libpython2.7.so"
+                pip uninstall -y protobuf
+                pip install -r ${PADDLE_ROOT}/python/requirements.txt
             elif [ "$1" == "cp27-cp27mu" ]; then
                 export LD_LIBRARY_PATH=/opt/_internal/cpython-2.7.11-ucs4/lib:${LD_LIBRARY_PATH#/opt/_internal/cpython-2.7.11-ucs2/lib:}
                 export PATH=/opt/python/cp27-cp27mu/bin/:${PATH}
                 PYTHON_FLAGS="-DPYTHON_EXECUTABLE:FILEPATH=/opt/python/cp27-cp27mu/bin/python
             -DPYTHON_INCLUDE_DIR:PATH=/opt/python/cp27-cp27mu/include/python2.7
             -DPYTHON_LIBRARIES:FILEPATH=/opt/_internal/cpython-2.7.11-ucs4/lib/libpython2.7.so"
+                pip uninstall -y protobuf
+                pip install -r ${PADDLE_ROOT}/python/requirements.txt
             elif [ "$1" == "cp35-cp35m" ]; then
                 export LD_LIBRARY_PATH=/opt/_internal/cpython-3.5.1/lib/:${LD_LIBRARY_PATH}
                 export PATH=/opt/_internal/cpython-3.5.1/bin/:${PATH}
                 export PYTHON_FLAGS="-DPYTHON_EXECUTABLE:FILEPATH=/opt/_internal/cpython-3.5.1/bin/python3
             -DPYTHON_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.5.1/include/python3.5m
             -DPYTHON_LIBRARIES:FILEPATH=/opt/_internal/cpython-3.5.1/lib/libpython3.so"
+                pip3.5 uninstall -y protobuf
+                pip3.5 install -r ${PADDLE_ROOT}/python/requirements.txt
             elif [ "$1" == "cp36-cp36m" ]; then
                 export LD_LIBRARY_PATH=/opt/_internal/cpython-3.6.0/lib/:${LD_LIBRARY_PATH}
                 export PATH=/opt/_internal/cpython-3.6.0/bin/:${PATH}
                 export PYTHON_FLAGS="-DPYTHON_EXECUTABLE:FILEPATH=/opt/_internal/cpython-3.6.0/bin/python3
             -DPYTHON_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.6.0/include/python3.6m
             -DPYTHON_LIBRARIES:FILEPATH=/opt/_internal/cpython-3.6.0/lib/libpython3.so"
+                pip3.6 uninstall -y protobuf
+                pip3.6 install -r ${PADDLE_ROOT}/python/requirements.txt
             elif [ "$1" == "cp37-cp37m" ]; then
                 export LD_LIBRARY_PATH=/opt/_internal/cpython-3.7.0/lib/:${LD_LIBRARY_PATH}
                 export PATH=/opt/_internal/cpython-3.7.0/bin/:${PATH}
                 export PYTHON_FLAGS="-DPYTHON_EXECUTABLE:FILEPATH=/opt/_internal/cpython-3.7.0/bin/python3.7
             -DPYTHON_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.7.0/include/python3.7m
             -DPYTHON_LIBRARIES:FILEPATH=/opt/_internal/cpython-3.7.0/lib/libpython3.so"
+                pip3.7 uninstall -y protobuf
+                pip3.7 install -r ${PADDLE_ROOT}/python/requirements.txt
            fi
+        else
+            pip uninstall -y protobuf
+            pip install -r ${PADDLE_ROOT}/python/requirements.txt
         fi
     fi
 
diff --git a/python/requirements.txt b/python/requirements.txt
index 5a70f1aa3ffc0ab6d4d148eb5bc26981784f2d32..6cbda1db545957b8e7b943366f9b954ff1dfdc77 100644
--- a/python/requirements.txt
+++ b/python/requirements.txt
@@ -1,6 +1,6 @@
 requests==2.9.2
 numpy>=1.12
-protobuf==3.1
+protobuf>=3.6
 recordio>=0.1.0
 matplotlib==2.2.3 # TODO: let python3 paddlepaddle package use latest matplotlib
 rarfile
diff --git a/tools/manylinux1/Dockerfile.x64 b/tools/manylinux1/Dockerfile.x64
index 48fd145e5fe6735fca3096752f801b1ec1cb39f0..c2fd743f62f536ab7443ca215d100478021d8f7c 100644
--- a/tools/manylinux1/Dockerfile.x64
+++ b/tools/manylinux1/Dockerfile.x64
@@ -31,10 +31,10 @@ RUN wget --no-check-certificate -qO- https://storage.googleapis.com/golang/go1.8
 ENV GOROOT=/usr/local/go GOPATH=/root/gopath
 ENV PATH=${GOROOT}/bin:${GOPATH}/bin:${PATH}
 
-# protobuf 3.1.0
-RUN cd /opt && wget -q --no-check-certificate https://github.com/google/protobuf/releases/download/v3.1.0/protobuf-cpp-3.1.0.tar.gz && \
-    tar xzf protobuf-cpp-3.1.0.tar.gz && \
-    cd protobuf-3.1.0 && ./configure && make -j4 && make install && cd .. && rm -f protobuf-cpp-3.1.0.tar.gz
+# protobuf 3.6.1
+RUN cd /opt && wget -q --no-check-certificate https://github.com/google/protobuf/releases/download/v3.6.1/protobuf-cpp-3.6.1.tar.gz && \
+    tar xzf protobuf-cpp-3.6.1.tar.gz && \
+    cd protobuf-3.6.1 && ./configure && make -j4 && make install && cd .. && rm -f protobuf-cpp-3.6.1.tar.gz
 
 RUN wget https://raw.githubusercontent.com/PaddlePaddle/Paddle/develop/python/requirements.txt -O /root/requirements.txt
 
diff --git a/tools/manylinux1/build_scripts/build.sh b/tools/manylinux1/build_scripts/build.sh
index 6c551eceb4543bf33229b9e5b5124522f3ee134c..5b676c024317596832870232dccb33895cae0c3e 100644
--- a/tools/manylinux1/build_scripts/build.sh
+++ b/tools/manylinux1/build_scripts/build.sh
@@ -17,7 +17,7 @@ OPENSSL_ROOT=openssl-1.1.0i
 OPENSSL_HASH=ebbfc844a8c8cc0ea5dc10b86c9ce97f401837f3fa08c17b2cdadc118253cf99
 EPEL_RPM_HASH=e5ed9ecf22d0c4279e92075a64c757ad2b38049bcf5c16c4f2b75d5f6860dc0d
 DEVTOOLS_HASH=a8ebeb4bed624700f727179e6ef771dafe47651131a00a78b342251415646acc
-PATCHELF_HASH=d9afdff4baeacfbc64861454f368b7f2c15c44d245293f7587bbf726bfe722fb
+PATCHELF_HASH=f2aa40a6148cb3b0ca807a1bf836b081793e55ec9e5540a5356d800132be7e0a
 CURL_ROOT=curl-7.49.1
 CURL_HASH=eb63cec4bef692eab9db459033f409533e6d10e20942f4b060b32819e81885f1
 AUTOCONF_ROOT=autoconf-2.69
@@ -107,11 +107,11 @@ curl-config --features
 rm -rf /usr/local/ssl
 
 # Install patchelf (latest with unreleased bug fixes)
-curl -sLO http://nipy.bic.berkeley.edu/manylinux/patchelf-0.9njs2.tar.gz
-check_sha256sum patchelf-0.9njs2.tar.gz $PATCHELF_HASH
-tar -xzf patchelf-0.9njs2.tar.gz
-(cd patchelf-0.9njs2 && ./configure && make && make install)
-rm -rf patchelf-0.9njs2.tar.gz patchelf-0.9njs2
+curl -sLO https://nixos.org/releases/patchelf/patchelf-0.9/patchelf-0.9.tar.gz
+check_sha256sum patchelf-0.9.tar.gz $PATCHELF_HASH
+tar -xzf patchelf-0.9.tar.gz
+(cd patchelf-0.9 && ./configure && make && make install)
+rm -rf patchelf-0.9.tar.gz patchelf-0.9
 
 # Install latest pypi release of auditwheel
 LD_LIBRARY_PATH="${ORIGINAL_LD_LIBRARY_PATH}:$(dirname ${PY35_BIN})/lib" $PY35_BIN/pip install auditwheel