Using the game cross efficiency model and game cross Malmquist index model improved, we estimate the innovation performance of 28 manufacturing industries in China from 2012-2015. The main results are as follows: ①From the result of static analysis, manufacturing innovation performance in China is relatively low, the difference about innovation performance in different manufacturing industry is obvious. ②From the result of dynamic analysis, Malmquist index of manufacturing innovation in China is in a state of negative growth, and is further decreasing. ③The root that Malmquist index of manufacturing innovation in China is weakly growing is relatively low technical change index. ④The difference about Malmquist index of manufacturing innovation in different manufacturing industry and its driving factors is obvious. Therefore, we need to enhance the technological progress level ，resolve production capacity, and optimize the model of innovation resource allocation in different manufacturing industry, to further enhance the innovation performance of manufacturing industry in China.