The implementation of green development has become an important choice for countries seeking the harmonious development of the economy and the environment. The National Ecological Civilization Pilot Zone is an innovative institutional mechanism for exploring green development in China. This study utilizes the National Ecological Civilization Pilot Zone policy as a quasi-natural experiment. Adopting data from 290 prefecture-level and above cities in China during 2014–2019 as the research object, this study matches the propensity score and improved differences-in-differences to assess the impact of green development mechanism innovation on regional total-factor environmental efficiency. The results show that this innovation had a significant impact on the improvement of total-factor environmental efficiency. Compared with non-pilot cities, the implementation of pilot zone areas contributed 16.78% to the growth of total-factor environmental efficiency in the experimental group cities. In addition, further analysis shows that mechanism innovation is more effective in areas with high pollution and high resource consumption. This study enriches the research on evaluation of the impact of innovation in green development mechanisms and provides a reference for further promoting pilot national ecological civilization zones.