Using the data of A-share listed companies in Shanghai and Shenzhen from 2010 to 2019, this paper constructs a two-way fixed utility model, panel Tobit model and instrumental variable method, and empirically tests the impact of government R&D subsidies on enterprise innovation performance based on the differences in economic region, enterprise scale and property right nature. It is found that government R&D subsidies have a significant incentive effect on enterprise innovation performance, and this positive promotion effect has time lag. From the perspective of the region where the enterprise is located, compared with the central and western regions, the government R&D subsidy has a stronger incentive effect on the economically developed eastern region.From the perspective of enterprise heterogeneity, the incentive effect of government R&D subsidies on the innovation performance of small and medium-sized enterprises is greater than that of large-scale enterprises, and the incentive effect on non-state-owned enterprises is greater than that of state-owned enterprises. This study provides corresponding policy suggestions for the government in the selection of funding objects and policy implementation.