Fiscal policy and monetary policy, as the two pillars of macro policy, play a significant role in promoting scientific and technological innovation. How to effectively coordinate these two policies is a key focus in both theory and practice. This article aims to explore the theoretical basis and practical characteristics of the synergy between fiscal support and financial support in scientific and technological innovation. For the important field of scientific and technological innovation, this paper analyzes the similarities and differences as well as the coordination mechanisms between fiscal support and financial support at the theoretical level. Meanwhile, it constructs a synergy model of fiscal support and financial support in scientific and technological innovation and conducts empirical tests. The research finds that the overall coordination degree of the composite system is on the rise, but there is still room for improvement in the synergy between fiscal support and financial support. Based on China’s practice, the main factors restricting synergy were analyzed. Policy suggestions for promoting the synergy of fiscal support and financial support were put forward. This research has reference value for understanding and promoting more effective utilization of the synergy between financial policies and fiscal policies to promote scientific and technological innovation.