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Based on the panel data of 11 provinces and cities in the Yangtze River Economic Belt from 2005 to 2018, this paper uses the SBM-DEA efficiency model with undesired output to measure the green innovation efficiency of the Yangtze River Economic Belt. The panel Tobit empirical analysis model was used to quantitatively analyze the impact of three different forms of government environmental regulations on the efficiency of green innovation. The research results show that the government’s mandatory environmental regulations and government financial subsidies for green innovation technology are two regulatory methods that positively promote the efficiency of regional green innovation, but government investment in environmental governance has a negative impact on the efficiency of regional green innovation. Then the study found that this negative impact has a significant inflection point effect: when it exceeds a certain threshold, the negative impact turns into a positive effect. At the same time, the impact of environmental regulations on the efficiency of green innovation has significant regional heterogeneity, and the three environmental regulations have a greater impact on downstream provinces and cities.