Considering the role of government, enterprises and market in regional innovation, the influence and mechanism of Chinese government''s science and technology expenditure on regional innovation capability are theoretically analyzed, and the panel data of 30 provinces and regions from 2008 to 2020 are used to test the impact effect and nonlinear relationship by systematic GMM model and threshold effect model. The results show that government science and technology expenditure has a significant incentive effect and positive lag effect on regional innovation capacity. The effect of government science and technology expenditure on regional innovation capacity is affected by the single-threshold effect of enterprise innovation performance and marketization, and there is a critical period for effectiveness to play. The research is helpful to clarify the relationship between the government, enterprises and the market in regional innovation, think about the form of government capital intervention in regional innovation, improve the efficiency of government science and technology expenditure, and enhance regional innovation capabilities.