Abstract: Based on the innovation value chain theory, dividing the regional innovation process into two sub-processes (innovation research and achievement transformation), we establish the conceptual model of the role of financial science and technology development in regional innovation. Considering the influence of the degree of regional openness, we study the affect mechanism of the two and we further analyze the regulatory role of regional policies and resource endowments. The results show that: the overall efficiency of regional innovation in China is low, mainly due to the inefficiency of regional innovation research. On the one hand, the development of financial science and technology has optimized the ecological environment of regional financial, and through the scale expansion of financial development, structural optimization and efficiency enhancement, regional innovation performance is promoted. On the other hand, financial science and technology improve the efficiency of innovation research through promoting regional trade and investment openness and promote the efficiency of innovation achievements transformation by promoting regional production openness. In the regions with balanced economic development, the efficiency of regional innovation research is higher; in the regions with unbalanced economic development, the efficiency of regional achievements transformation is higher. At present, China’s innovation supportive policies are mostly to promote the achievements transformation rather than innovation research, thus the policy is relatively ineffective. Based on the above analysis results, the effect of the development of financial science and technology in regional financial ecology and regional openness can be guided better to improve the efficiency of regional innovation.