Inclusive green development aims to ensure sustainable economic growth while promoting social equity and resource and environmental improvement. It is an inevitable choice for building ecological civilization and improving people's livelihood. This study constructed an evaluation system of inclusive green efficiency, and used the Super-Epsilon-Based Measure (EBM) model considering the undesirable outputs to comprehensively measure China's inclusive green efficiency. On this basis, spatial autocorrelation analysis was used to analyze the spatiotemporal characteristics of inclusive green efficiency. By using a spatial Durbin model, the spatial spillover effects and influencing factors were analyzed. The results show that: 1) From 2000 to 2017, China's comprehensive inclusive green efficiency and scale efficiency fluctuated slowly, and the pure technical efficiency showed a "V-shaped" trend. The improvement of comprehensive efficiency gradually changed from scale effect to technology driven. 2) The spatial pattern of inclusive green efficiency in China has evolved from low-level equilibrium to high-level imbalance. The high-value areas are concentrated to the east of the Hu Huanyong Line, while the low-value areas are mainly in the northwestern, southwestern, and northeastern areas. Comprehensive efficiency and pure technical efficiency form three high-value areas in Beijing-Tianjin, the Yangtze River Delta, and the Pearl River Delta at the national level, and the high-value areas of scale efficiency show a "H" shape. 3) The same type of inclusive green efficiency shows the characteristics of spatial agglomeration, which is also continuously enhanced. The hotspots tend to move to the northeast. The hotspots are gradually stabilized in the Yangtze River Delta region, and the secondary hotspots are mainly in the Beijing-Tianjin and Pearl River Delta regions. The northwest, southwest, and northeast are basically cold spots. 4) The regression results of spatial Durbin model show that there is a positive spatial spillover effect of comprehensive inclusive green efficiency and its components. Economic development level, industrial structure, industrialization, government administrative ability, fiscal decentralization, environmental regulation, scientific and technological innovation, and marketization have significant influences on inclusive green efficiency, among which government administrative ability, fiscal decentralization, environmental regulation, scientific and technological innovation, and marketization have some spillover effects. Finally, some related policies, such as strengthening inter-regional exchanges and cooperation, accelerating the optimization and upgrading of industrial structure, optimizing the government's fiscal expenditure structure, promoting the transformation and application of scientific and technological achievements, and letting the market play a decisive role in the allocation of resources, were put forward based on the empirical analysis. This study provides a new perspective than the traditional assessment of economic efficiency, and the conclusions can provide some reference for China's ecological civilization construction and green transformation development.