Efficiency evaluation of R&D is a very important part of R&D management in enterprises, but the design and choice of evaluation method is the most difficult. This paper uses DEA method to analyze R&D efficiency of the specimen, based on the listed companies of biochemical and pharmaceutical. The results indicate that the span of R&D efficiency of most listed biochemical and pharmaceutical companies is very little, the R&D efficiency has relationship with the companies size to some extent, the R&D expense of some companies is more efficient than the R&D staff expense. Meanwhile it is improved that the DEA method is suitable for the R&D efficiency evaluation.