Based on the panel data of 30 provinces in China and the SBM-Malmquist-Luenberger model, a comprehensive evaluation of all-factor green energy efficiency in each province is conducted. It is found that the energy structure and all-factor green energy efficiency in southeast China are significantly higher than those in central and western China. On this basis, this paper empirically tests the impact of the pilot policy of emission trading on total factor green energy efficiency in 2008 by using the double difference method. The research shows that the emission trading system can significantly improve the regional total factor green energy efficiency; further research finds that green technological innovation is the main path for the policy to promote green total factor energy efficiency; heterogeneity analysis shows that in the high pollution pilot areas, the emission trading system plays a more significant role in promoting all-factor green energy efficiency and green technology innovation.