Based on the hypothesis that industry structure and financial develop is positively related with regional innovation performance, this thesis uses a panel data set of China’s 31 provinces and municipal cities from year 2004 to 2013 to explore the impact of industry structure and financial development on regional innovation performance by Zero-Truncated Negative Binomial Regression Model (ZTNbreg). The results indicate that: (1) Industry structure negatively relates with regional innovation performance; (2) Financial development also negatively relates with regional innovation performance. Further study shows that: (1) There is a significant substitute effect between industry structure and financial development; (2) The impact of industry structure and financial development on regional innovation performance varies among China’s eastern, middle and western regions. In view of above research results, this thesis draws some conclusions and enlightenment.