Taking 28 listed companies in China’s A-share pharmaceutical manufacturing industry from 2018 to 2021 as samples, with tax incentives as an explanatory variable, R&D investment intensity as an intervening variable, enterprise size, enterprise establishment time, return on total assets, debt-to-assets ratio, and fixed asset density as control variables, and innovation performance as explained variable, a multiple linear regression model is established, and descriptive statistics, correlation analysis, multicollinearity test, and robustness test are carried out to empirically analyze the influence of tax incentives on the innovation performance of pharmaceutical manufacturing enterprises. The results show that tax incentives have a significant positive impact on the innovation performance of pharmaceutical manufacturing enterprises, and tax incentives can promote pharmaceutical manufacturing enterprises to increase the intensity of R&D investment, and the intensity of R&D investment has a certain mediating effect and long-term influence on the relationship 1between tax incentives and innovation performance. Combined with the empirical results, the paper puts forward the strategy of improving enterprise innovation performance to enhance the core competitiveness of enterprises.