Based on 30 provincial data from 2000 to 2009, and by using STATA, the relation between market competition, government R&D input, intellectual property rights protection and regional innovation performance in China was investigated in the paper. This study found out that: (1) reducing local protection is positively related to regional innovation performance but the effect of non-state-owned economy development degree is not significant. (2) From the point of government behavior, the protection of intellectual property rights will improve regional innovation performance, but R&D investment will have a negative effect on regional innovation performance. This paper analyzes the reasons and puts forward countermeasures and suggestions to improve regional innovation performance.