With the deepening of innovation driven and highquality development strategies, it is increasingly important to improve the effectiveness of fiscal innovation subsidies for enterprise innovation incentives. Using the data of Shanghai and Shenzhen A-share non-financial listed companies from 2008 to 2023, this paper uses the propensity score matching method to analyze the differences in the effectiveness of fiscal innovation subsidies in stimulating the internal driving force of enterprise innovation and stimulating the innovation output of enterprises. The research finds that different types of fiscal innovation subsidies have significant differences in the effectiveness of enterprise innovation incentives. The overall impact of financial innovation subsidies for the transformation of scientific and technological achievements is the largest, and the incentives for enterprise invention patents are stronger. There are also significant differences among different enterprises, with subsidies for technology achievement transformation and technology funding having the greatest impact on large enterprises, and subsidies for technology talent support and technology achievement transformation having the greatest impact on small and medium-sized enterprises. Therefore, we suggest to improve the support of financial innovation subsidies for the transformation of scientific and technological achievements. The subsidies for science and technology funds support should focus on large and medium-sized enterprises, concentrate on tackling cutting-edge technologies. Subsidies for supporting scientific and technological talents should be appropriately tilted to scientific and technological personnel in small and medium-sized enterprises.