This study used Super-SBM model considering the undesirable outputs to measure inter-provincial green inclusive efficiency in China, analyzed the spatial and temporal changes and the influencing factors by panel Tobit model during 2000 to 2016. The results showed that green inclusive efficiency considering both social and eco-environmental factors was significantly lower than that only considering social factors. Green inclusive factors had significant impacts on the measurements. From 2000 to 2016, the inter-provincial green inclusive efficiency in China showed a trend of U-shaped evolution with obvious staged characteristics. The absolute and relative differences of green inclusive efficiency between provinces were expanding. China's inter-provincial green inclusive efficiency showed an unbalanced spatial pattern. There were three high-efficient agglomeration areas in the whole country: Beijing-Tianjin, the Yangtze River Delta, and the Pearl River Delta. The low-efficient types were scattered in the southwestern, northwestern, northern China, as well as in the middle and lower reaches of the Yangtze River. To comprehensively improve green inclusive efficiency, it should take more measures by promoting the optimization and upgrading of industrial structure, upgrading the level of macro-control of local governments, optimizing the import and export structure, fully considering the role of the market, and improving the level of scientific and technological innovation.