In order to study the impact of external financing structure differences and government subsidies on enterprises’ innovation performance, this paper uses fixed effect model to analyze the panel data of listed manufacturing enterprises from 2015 to 2018 in China. The results show that: The combination of short-term loans, long-term loans and government subsidies failed to have a significant incentive effect on enterprises’ innovation performance. On the contrary, enterprises issuing bonds will enhance the incentive effect of government subsidies on innovation performance. Further analysis find that: the increase of the proportion of equity financing will have a more obvious positive impact on innovation performance, but the effect of government subsidies will be weakened. Once the government subsidies exceeded the critical value, the effect will change from incentive to inhibition. In the future, government decisions should strengthen the support of Small & Micro Enterprises and reduce the distortion of enterprises’ financing behavior. Enterprises should rationally adjust their financing decisions, promote the organic combination of government subsidies and the positive role of financing, and promote the ability of scientific and technological innovation.