Abstract: In order to make full use of the science and technology resources of western region, and improve the efficiency of investment in science and technology, we use data envelopment analysis (DEA) to estimate the relative efficiency of the input-output in science and technology in this paper. The result shows that the relative efficiency of the input-output in science and technology is valid in Chongqing, Gansu and Qinghai, but it is invalid in the Yunnan, Guangxi, Ningxia and Inner Mongolia Autonomous Region. Then it analyzes the current status of investment in science and technology of western region, and puts forward some policy proposals.