The innovation efficiency of high patent intensity industry affects independent innovation ability and competitiveness of the industry. This paper uses DEA-Malmquist index analysis method to make an empirical analysis on the innovation efficiency and the influencing factors of our national high patent intensity industry. From the analysis, we learn that the scale efficiency of the high patent intensity industry is not very high, but the innovation efficiency of the whole industry is improving. On this basis, we use the Tobit regression model method to analyze the influencing factors of innovation efficiency of high patent intensity industry. As a result, we find that the government support, the level of the industry’s technology, the scale of enterprises, the qualities of relative employees have positive correlations with the innovation efficiency. Besides, the industry agglomeration degree has a negative correlations with the innovation efficiency. Finally, combining of the above analysis, we make proposals to improve the innovation efficiency of high patent intensity industry.