China is the most populous country in the world, and agriculture has played a large role in the country’s remarkable economic achievements. However, the high levels of pollution and emissions from agriculture pose a threat to the nation’s food and ecological security. Using a global weighted Russell distance function model, this paper attempts to provide strategies for the green development of China’s agriculture by investigating the historical green total factor productivity. The results show that (1) during the sample period, China’s agricultural green total factor productivity (AGTFP) showed a u-shaped trend, and the turning point was 2010. Technological progress in terms of agricultural output, energy use and pollutant treatment was the most powerful factor of growth after 2010, while the technological retrogression in terms of capital use was the main obstacle to growth. (2) Eastern China has the highest AGTFP, while western China has the highest AGTFP growth rate. This result indicates that eastern China is a leader in green agricultural development, while green agricultural development in western China is the most promising. The “mid-China collapse” occurred in the central China agricultural area. The collapse of the central region was mainly caused by a decline in pure technical efficiency; more specifically, the pure technical efficiency of fertilizer severely restricted the sustainable agricultural development of this area. (3) The provinces that have great spatial differences in terms of agricultural development and the driving factors of AGTFP can develop suitable green agricultural evelopment strategies based on the results presented in this study.