Abstract: Strengthening the basic research is to enhance the original innovation ability and the independent innovation source supply.It is a critical approach to promote China to an innovative and leading nation in science and technology in the world.To this aim,the state council has made clear that “innovation is the first step to achieve the optimization and development of the eastern region and to promote the differentiation and leap-forward development of the central and western regions”.And to implement this regional “differentiation” and “leapfrog” innovation strategy,the first step is to deal with the efficiency objective measurement and difference analysis of basic research innovation,and then to promote regional allocation of resources to achieve optimization.Envelope analysis of SBM-BBC model of output oriented to “The Tenth Five-Year”,“The Eleventh Five-Year ”,“The Twelfth Five-Year” period with an exception of Tibet in mainland China eastern,central and western areas of basic research innovation efficiency of the differences showed the following results:(1)The average efficiency of basic research innovation in the east was better than in central and western regions in the three periods.The eastern region includes Beijing,Shanghai,Zhejiang,Guangdong,and Jiangsu.(2)In the western regions such as Ningxia and Qinghai,after the development strategy of the western region during the “The Tenth Five-Year Plan ”period,the innovation efficiency of basic research in the three periods was significantly improved.(3)There are quite a number of input-output imbalances,which leads to innovation inefficiency in some areas.Therefore,it is important to strengthen the basic research and development with a better allocation of resources in the eastern region to make it a “leading force” in the basic research innovation.The mid-central region as the “intermediate power”,it is important to support and cultivate its basic research and innovation.With a comparatively weak foundation,the western region can be made a “reserve force”for the basic research in China.

Key words: basic research innovation efficiency, envelope analysis method, measurement of innovation efficiency, input and output structure