Taking 30 provinces in China as the research object, the super-efficient SBM model is used to calculate the carbon emission reduction efficiency of green hydropower from 2010 to 2019. The hierarchical cluster analysis is used to compare regional differences. And then, the within-group inequality, between-group inequality and their contribution to the overall inequality are calculated by using Theil index. Finally, the Malmquist index is used to decompose and analyze the efficiency. The results show that the development efficiency of green hydropower in China is the highest in the west, followed by the middle and the lowest in the east. The within-group inequality of efficiency is higher than the between-group inequality, and the development inequality of eastern provinces contributes the most to the overall inequality. Except for the scale efficiency, all the other efficiencies have increased. Therefore, it is necessary to rationally arrange hydropower development, attach importance to inter-provincial complementary cooperation and expand hydropower scale.