Stimulating enterprise innovation is an important way for the state to promote economic development and social progress. Using data from listed manufacturing companies on the Shanghai and Shenzhen stock exchanges in China from 2010 to 2022, this paper analyzes the impact mechanism of R&D subsidies and intellectual property protection on enterprise independent innovation inputs and empirically tests the relationship between government R&D subsidies, intellectual property protection, and enterprise independent innovation inputs. The study finds that R&D subsidies exert a suppressive effect on enterprise independent innovation inputs, while intellectual property protection exerts an incentive effect. At the same time, R&D subsidies and intellectual property protection have an interactive effect on enterprise independent innovation inputs, and the level of intellectual property protection can weaken the suppressive effect of R&D subsidies on enterprise independent innovation inputs. The heterogeneity analysis shows that the suppression effect of R&D subsidies on enterprise independent innovation inputs is stronger in state-owned enterprises and enterprises with weaker market competition, while the incentive effect of intellectual property protection is stronger in non-state-owned enterprises and enterprises with stronger market competition. Further research reveals that R&D subsidies can only promote the quantity of enterprise innovation output, while intellectual property protection can improve the quality of enterprise innovation output and incentivize substantive innovation, which indicates that the inhibitory effect of R&D subsidies on enterprise autonomous innovation input is the key factor causing enterprises to prioritize innovation output “quantity” over “quality”