Abstract: In the context of the market-oriented reform of rural factors, it is of great significance to promote the flow, optimization and reorganization of factors to promote the green development of agriculture. For a long time, agricultural development has been under the severe situation of dual constraints on resources and environment, and it is urgent to change the mode of agricultural development. Therefore, it is necessary to solve the problem of resource allocation with marketization, solve the problem of environmental pollution with policy regulation, realize the transformation of agriculture from traditional extensive to green and efficient, and build a new pattern of agricultural green development that takes into account sustainable growth and high-quality development. This study focuses on the marketization of agricultural production factors, and explores the relationship and mechanism between the marketization of agricultural factors and agricultural green production efficiency. Based on the panel data of 31 provinces from 2001 to 2021, this paper uses the two-way fixed-effect model, the IV-2SLS model and the dynamic spatial Durbin model to study the impact of agricultural factor marketization on agricultural green production efficiency, explore the moderating effect of environmental regulation and the mediating effect of factor endowment structure, and further analyze the regional heterogeneity and spatial spillover effect of agricultural factor marketization on agricultural green production efficiency. The results show that: 1) The marketization of agricultural factors has a significant positive impact on the improvement of agricultural green production efficiency. After endogeneity treatment and robustness test, this conclusion is still valid. 2) Environmental regulation plays a positive moderating role in the impact of marketization of agricultural factors on agricultural green production efficiency. Among them, the command-and-control and market-incentive environmental regulations impose mandatory constraints on market economy entities based on administrative and economic means, respectively, which have a significant positive regulatory effect. 3) The marketization of agricultural factors has an impact on the green production efficiency of agriculture by optimizing the factor endowment structure. The endowment structure of land factors and the endowment of labor factors were significantly negative, while the endowment of capital factors was significantly positive. This means that factor endowment input has gradually changed from land-intensive and labor-intensive to capital-intensive. 4) The impact of marketization of agricultural factors on agricultural green production efficiency is regionally heterogeneous, and the impact effect in the eastern region is significantly higher than that in the central and western regions. 5) The impact of the marketization of agricultural factors on agricultural green production efficiency has a spatial spillover effect. Therefore, the following policy suggestions are put forward: First, deepen the market-oriented reform of agricultural factors and improve the efficiency of the allocation of production factors. Second, strengthen the intensity of environmental regulation in the agricultural sector to ensure that the input of production factors meets environmental protection requirements. Third, it is necessary to establish and improve the price mechanism of the factor market, and guide agricultural producers to make factor inputs based on price signals. Fourth, we should pay attention to the differentiated development between regions, and the eastern region will further promote the market-oriented reform of factors, and the central and western regions will gradually promote the market-oriented reform of factors according to the actual situation. Fifth, it is necessary to strengthen the integration of agricultural factor markets between regions and promote the cross-regional flow of production factors.