Abstract： R&D efficiency is the mark for the innovation performance. The R&D efficiency of 17 manufacturing industries ill China during the 10th Five-Year Plan period (2001-2005) is analyzed based on a super-efficiency Data Envelopment Analysis(DEA) model，and the utilization ratio of R&D input is analyzed. The results show that more than 60% of manufacturing industries had a lower efficiency, and only a few of them have improved their efficiencies during this period, others just showed an erratic fluctuation of R&D efficiency. On the basis of the empirical analysis, some suggestions for improving the R&D efficiency of Chinese manufacturing industries are put forward.