Abstract: The construction of modern agricultural management system will become a new driving force to promote the green development of agriculture, and sorting out its influence mechanism will be of great significance to transform agricultural production mode and realize modern and efficient agriculture. Based on the panel data of 31 provincial administrative units in China from 2011 to 2022, this paper uses entropy method and SBM model respectively to measure the development level of China's modern agricultural management system and agricultural green production efficiency. Through two-way fixed effect model, heterogeneity test and threshold effect analysis, the modern agricultural management system to promote the improvement of agricultural green production efficiency was empirically analyzed. The results showed that both modern agricultural management system and agricultural green production efficiency showed an upward trend in recent years, and they were similar in temporal and spatial distribution. The development of modern agricultural management system can promote the improvement of agricultural green production efficiency, and its effect is mainly achieved by promoting the progress of green technology. From the sub-dimension, the output index has the strongest influence. In terms of regions, the influence coefficient of central and western regions is larger, the eastern region is the smallest, the influence coefficient of main grain producing areas and main sales areas is smaller, and the production and marketing balance area is the largest. Through the threshold model verification, it can be seen that the modern agricultural management system has a non-linear impact on the agricultural green production efficiency, that is, with the development of social economy and the improvement of the development level of agricultural economy, the utility of the modern agricultural management system will show a diminishing marginal utility. This study provides a feasible path and policy basis for realizing the transformation of agricultural green development.