At present, social capital is considered to be one of the important reasons for promoting economic development and causing regional economic differences, but in the existing research, there is little literature on the impact of regional social capital on enterprises’ green innovation behavior and green total factor productivity (GTFP), so this paper aims to enrich the research in this area. This paper builds a regional social capital evaluation index system and uses the super-SBM model to measure the enterprise GTFP. Then, this paper brings regional social capital, enterprise green innovation and GTFP into a unified framework for the first time and further reveals the quantitative relationship between the three by using OLS and Tobit two-step methods based on the panel data of 30 provinces from 2011 to 2019. The results show that regional social capital has a positive effect on enterprise GTFP and green innovation (except for strategic green innovation output), enterprise green innovation output has a positive role in promoting GTFP, and enterprise green innovation capital investment has a masking effect between regional social capital and GTFP. Furthermore, the expansive study finds that there are differences in the impact of regional social capital on green innovation and the GTFP of heterogeneous enterprises, and financing constraints have a positive regulatory effect on the relationship between regional social capital and the GTFP of state-owned enterprises, while having an inhibitory effect on the GTFP of private enterprises. Fiscal decentralization has a partial mediating effect between regional social capital and enterprise GTFP, while urbanization and CO2 emissions have a masking effect. Additionally, this paper aims to provide a reference for the improvement of regional social capital theory, the strategic choice of green innovation of enterprises, and the high-quality development of the economy.