Taking the data from 2011 to 2015,the article builds innovative input-output index system and uses DEA method to analyze R&D level of industrial enterprises by overall efficiency, technical efficiency and scale efficiency to evaluation and comparison from the angle of horizontal and vertical, and the redundancy value analysis to optimize overall efficiency. The research shows that the R&D efficiency of Chinese industrial enterprise is in the middle level and there is still a big space to improve. There are obvious regional differences in the research and innovation activities of industrial enterprises and some regions are unbalanced. Based on these results, the paper puts forward some recommendations.