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Because of the limitation of resources, we need enhance the inputs on R&D, education, new technology application, and so on, to get the power on regional competition. We will introduce as comprehensive evaluation method, named as AHP-TOPSIS, to measure the performance of regional innovation system in China. Based on the calculation results, 30regions in China were ranked based on different levels (Lower level, intermediate level and higher level) in the performance of their regional innovation system. The corresponding developing strategies and measurements for different levels were proposed in this paper.