High efficient innovation-driven is very important to developing country with limited resources, but the research related Regional Innovation System(RIS) innovative driving impetus in China is quite weak, let alone the quantitative analysis to input-output of each subject in RIS. For the first time, the paper, by means of co-integration method, establishes model and does empirical analysis on performance of RIS with some indexes as government's R&D input and cooperative intensity among industries, universities and research as well as the role and status of small and medium-sized enterprises(SMEs). It is found that no matter from short-term perspective or long-term perspective, government's direct intervention is significant to innovation performance; but the promoting function of the cooperative intensity among industries and universities as well as research to innovation is not shown up, besides, the R&D input elasticity of SMEs in RIS is only 0.0547 in the short term, but SMEs has the greatest elasticity in the long run. Finally, the research conducts thorough analysis and accordingly puts forward some suggestions.\