This paper explores the synergy effect of the government subsidies, tax incentives, and government procurement on innovation based on synergy theory, and further analyzes its path and mechanism in the process of innovation. We find that government subsidies, tax incentives, and government procurement exert positive synergy effect on innovation. Furthermore, in the process of innovation, government subsidies are shown to play strongest roles in the stages of innovation input and technological development, while government procurement is the most crucial in the transformation stage of technological innovation, and tax incentives play balanced roles. We also find that innovation resource input, innovation technology spillover, and innovation cooperation all play partial mediating roles in the synergy effect of science and technology policies on innovation. This paper applies the synergy theory to the field of innovation policies, which enriches and expands relevant researches, and provides micro-evidence for in-depth understanding of the effect of science and technology policies on innovation.