The positive development of ecological efficiency is of great significance to the coordinated development of economy and ecological environment. In order to study the temporal and spatial distribution dynamics and regional differences of the ecological efficiency of China's six important geographic regions, this paper uses the Super-SBM model to calculate the provincial ecological efficiency of China from 2005 to 2020, and uses the kernel density function, Gini coefficient, σ convergence and Markov transition matrix to analyze the dynamics of spatial distribution and regional differences. The results show that:(1) China's overall ecological efficiency decreased first and then increased. Beijing, Qinghai, Guangdong, Hainan, Shanghai, Jiangsu, Fujian, Henan, and Yunnan have developed better ecological efficiency. (2) The overall difference in eco-efficiency is large, inter-regional differences and hypervariable density are the main sources of overall differences. There are differences in spatial distribution. The eco-efficiency of North region has developed well, while the eco-efficiency of Northeast region is the lowest. The Northwest region has the largest internal differences and the most unbalanced development; the Northeast region has the smallest regional differences, and both have poor development. The eco-efficiency development in China does not have the characteristics of convergence. (3) The national and regional eco-efficiency has the greatest transfer probability from year t to year t+1 to the same level of eco-efficiency.