Government R&D subsidy is one of the important means to overcome R&D market failure and promote enterprise R&D activities. However, studies examining the complex relationship between government R&D subsidies, financing constraints and ownership nature on enterprise innovation performance are rare. This study is based on the data of listed manufacturing enterprises in China from 2001 to 2018. The results show that: first of all, the impact of government R&D subsidies and financing constraints on the innovation performance of enterprises depends on the nature of enterprise ownership, and the innovation performance of state-owned enterprises is significantly affected by it. Second, the financing constraints of enterprises will be eased after they receive government R&D subsidies. Compared with state-owned enterprises, the government R&D subsidy has a stronger effect on the financing constraints of private enterprises. Finally, for any ownership enterprise, government R & D subsidies will crowd out R & D investment.