With the deepening of globalization and knowledge economy era coming，innovation capability is increasingly becoming an important determinant of regional competitiveness. The purpose of this article is checking the regional innovation capacity and regional innovation differences in china，and then finding out the factors that affect regional innovation differences. Firstly，the article constructed innovation input and output evaluation index systems，and the innovation output quantity and innovation efficiency were selected to present regional innovation performance. Then the article analyzed the regional differences and spatial distribution of innovation performance and innovation efficiency. The result shows that the order of regional differences of different index is as follows，Innovation output >innovation Performance > innovation efficiency. In addition，the high value area of innovation performance are eastern coastal zone and along the Yangtze River region，which coincides with the economic development preferentially region proposed by the T-shaped theory. Finally，we investigated the factors including Common innovation infrastructure，the cluster-specific innovation environment，the quality of linkages，government supporting and technology spillover that affect the regional innovation performance. Then we conducted regression analysis to examine the relationships between regional innovation performance and nine influencing factors. The result reveals that common innovation infrastructure influences regional innovation performance most. Government supporting，cluster-specific innovation environment and technology spillover affect regional innovation performance less than common innovation infrastructure. There are two sides’ effects of the international spillovers on regional innovation performance.