Abstract: Under the realistic demand of economic and environmental sustainable development, it is of great significance to effectively evaluate the actual level of green output efficiency under the constraint of resources and environment to promote the improvement of energy conservation and emission reduction policies. In this paper, regional external environment and technical management factors are taken into account, and a three-stage DEA model is used to measure the true green output efficiency level, change trend and characteristics of 31 provinces and cities in China from 2011 to 2017, and a three-stage ML index is used for dynamic comparative analysis. The results show that: (1) the green output efficiency level shows a downward trend, from high to low: central, eastern, national, One Belt and One Road and western regions, which are the same as the adjusted results, but the regional difference is increasing, and scale efficiency is still the main factor restricting the improvement of green output efficiency. (2) The overall green output efficiency after excluding environmental factors is overestimated to varying degrees. Among them, the eastern region is stabilized by the support of pure technical efficiency, the leading green output efficiency in the central region is derived from the growth of scale efficiency, while the improvement of the green output efficiency in the western region comes from favorable environmental management factors. (3) After the adjustment, more provinces reach the green output efficiency frontier, and all of them are in the scale efficiency frontier and the provinces with constant scale return account for about 1/3. Different environmental factors in different regions have different paths to influence the green output efficiency, so it is necessary to combine their own development characteristics, give full play to the scale effect and enhance the level of pure technical efficiency, so as to improve the green output efficiency.