China’s agricultural economy is developing rapidly, but the unbalanced regional development is still a key issue that needs to be discussed today. By studying the total factor productivity of green agriculture and its factors, this paper analyzes the regional differences in time and space changes between the eastern, central and western parts of China. In this paper, the total factor productivity of green agriculture is calculated and decomposed by Metafrontier Malmquist-Luenberger index based on directional distance function. The results are as follows: First, the total factor productivity level of green agriculture in China is increasing year by year, but the overall level is still at a low level and has greater volatility; Second, although the total factor productivity of green agriculture shows an upward trend, the three regions show a downward trend in turn, which has great differences; Third, there are obvious differences in technological efficiency, optimal production potential and technological gap between the eastern, central and western regions, and there are great differences in productivity among regions and provinces. Based on the results, this paper puts forward policy recommendations, according to the regional heterogeneity, from a number of angles to rely on the joint efforts of many parties to improve the level of total factor productivity of green agriculture.