Since the reform and opening up, China’s high-speed economic growth mainly depends on the inputs of production factors, but with the rising cost of production factors and the tightening constraints of resources and environment, the traditional economic development model is no longer sustainable. Under the new development stage and new development concept, scientific and technological innovation will become the core driving force for future economic growth. However, the characteristics of large investment, long cycle, and high risk of innovation activities lead to the lack of core power of enterprises’ innovation. In this case, government is an important driving force for enterprises’ innovation and development. Scientific evaluation of the influence and mechanism of government financial support on enterprises’ innovation activities is of great practical significance for improving the effectiveness of macroeconomic fiscal policies, enhancing the innovation ability of enterprises, and promoting the development of China in science and technology and high-quality development. Based on the innovation output data of A-share listed companies from 2015 to 2020, this paper examines the impact of financial investment in science and technology on the innovation outputs of enterprises and the corresponding mechanism. The findings of the article are as follows. Firstly, the intensity of financial investment in science and technology has a significant positive impact on the quantity and quality of innovation outputs of enterprises, and this conclusion is still valid after a series of robustness tests and endogeneity problems. Secondly, mechanism analysis shows that increasing financial investment in science and technology can ease the financing constraints of enterprises and enhance the willingness to innovate, thus promoting the growth of the enterprise’s innovation outputs. Thirdly, heterogeneity analysis shows that increasing financial investment in science and technology has a greater promoting effect on the innovation outputs of non-state-owned enterprises and enterprises with strong absorptive capacity. Distinguishing the characteristics of industries, it is found that increasing financial investment in science and technology has a greater role in promoting the innovation output of enterprises in high-tech industries, competitive industries, capital-intensive and technology-intensive manufacturing industries. By dividing the scale of government expenditure on science and technology, it is found that in areas with a smaller scale of expenditure on science and technology, increasing financial investment in science and technology has a greater promoting effect on the quantity and quality of enterprises’ innovation outputs. Compared with previous literature, this paper expands on the following two aspects. Firstly, it discusses the influence of financial investment in science and technology on enterprises’ innovation outputs from a macro perspective, analyzes the corresponding mechanism, and broadens the previous literature on the impact of enterprise innovation output. Secondly, different from previous literature on external boundary conditions of enterprises’ innovation outputs, this paper examines the effects of enterprises’ absorptive capacity and industry differences, and discusses in detail the heterogeneous effects of enterprises’ industry characteristics according to whether they are high-tech enterprises, competitive enterprises, manufacturing enterprises, and capital-intensive and technology-intensive manufacturing enterprises. To a certain extent, the research in this paper reveals the differential impact of financial investment in science and technology on enterprises’ innovation outputs and internal logic, which is helpful for government departments to improve the efficiency and accuracy of fiscal and tax policies to support enterprises’ science and technology innovation, and better guide enterprises’ innovation and development.