This paper uses green innovation and environmental pollution as the mediating variables to construct a mediating effect model to investigate whether China's carbon emission trading policy can improve regional eco-efficiency by reducing regional environmental pollution and stimulating green innovation. This study is based on panel data from 30 provinces and municipalities directly under China's central government and autonomous regions from 2003 to 2019. The eco-efficiency of these provinces is measured using the super-efficiency DEA model and the difference-in-difference method (DID). The results show that (1) China's emission trading policy significantly improves regional ecological efficiency and the per capita GDP. The improvement can effectively improve regional ecological efficiency. (2) The mediating effect of green innovation and environmental pollution is significant. That is, China's carbon emission trading policy further improves regional ecological efficiency by stimulating more green innovation and reducing the synergy brought by environmental pollution. (3) There are differences in the feedback of this impact mechanism between different regions: It shows the characteristics of the western region being more significant than the eastern region. The central region has no significant effect. The research conclusion can provide a policy reference for the subsequent unified promotion of the construction of a carbon emission trading market nationwide and a theoretical basis for helping to achieve the "dual carbon" goal.