Abstract: Efficient regional innovation system is the key to improve the overall efficiency of national innovation system. Based on the functional perspective of innovation system, this paper constructs a theoretical model of innovation system efficiency in district construction of "subject-environment", and analyzes the improvement path of regional innovation system efficiency during the 13th Five-Year Plan period. The results show that a single condition cannot form high efficiency or low efficiency of regional innovation system. Through the interaction between subjects and environmental functions, three types of efficiency improvement paths are constructed: inclusive entrepreneurial innovation system, financial service innovation system and technological self-circulation innovation system. Among them, inclusive entrepreneurial innovation systems include middle and low-end labor-intensive entrepreneurial regional innovation systems and internal circulation production-intensive entrepreneurial regional innovation systems; Financial service-oriented innovation system includes two types: self-circulating financial regional innovation system and export-oriented financial service regional innovation system. In the future, we should focus on improving the efficiency of the regional innovation system, building a regional innovation system according to local conditions, promoting entrepreneurship, strengthening financial support for innovation and enhancing scientific and technological research capabilities.