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 30 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. The influence of modern agricultural management system on agricultural green production efficiency was empirically analyzed by two-way fixed effect model, heterogeneity test and threshold effect analysis. The results show that the development of modern agricultural management system can promote the improvement of agricultural green production efficiency, and this result is still valid after a series of robustness tests and instrumental variables tests. The modern agricultural management system has no significant effect on the efficiency of agricultural green technology, but promotes the progress of agricultural green technology. From the perspective of different regions, the greater the topographic relief, the more difficult it is for modern agricultural management system to play its role in promoting the green development of agriculture. The better the development of the digital economy, the more the modern agricultural management system can promote the improvement of agricultural green production efficiency. The threshold model is further verified to show that the modern agricultural management system has a non-linear impact on the agricultural green production efficiency. On the one hand, with the development of social economy, the utility of the modern agricultural management system becomes stronger; on the other hand, with the improvement of the development level of agricultural economy, the marginal utility of the modern agricultural management system will decrease. This study provides a feasible path and policy basis for constructing modern agricultural management system and realizing the transformation of agricultural green development.