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. Agricultural development has long been under severe dual constraints on resources and environment, and there is an urgent need to change the mode of agricultural development. Therefore, it is necessary to address the problem of resource allocation through marketization, address the problem of environmental pollution through policy regulations, realize the transformation of agriculture from traditional extensive mode to green and efficient mode, and build a new pattern of agricultural green development that considers sustainable growth and high-quality development. This study focused on the marketization of agricultural production factors and explored the relationship and mechanism between the marketization of agricultural factors and agricultural green production efficiency. Based on panel data from 31 provinces from 2001 to 2021, this study used the two-way fixed-effect model, instrumental variables two-stage least squares (IV-2SLS) model, and dynamic spatial Durbin model to study the impact of agricultural factor marketization on agricultural green production efficiency, explored the moderating effect of environmental regulation and the mediating effect of factor endowment structure, and further analyzed the regional heterogeneity and spatial spillover effect of agricultural factor marketization on agricultural green production efficiency. Results were as the following: 1) The marketization of agricultural factors had a significant positive impact on the improvement of agricultural green production efficiency. This conclusion was valid after endogeneity treatment and robustness testing. 2) Environmental regulation played a positive moderating role in the impact of marketization of agricultural factors on agricultural green production efficiency. Command-and-control and market-incentive environmental regulations imposed mandatory constraints on market economy entities based on administrative and economic means, respectively, which had significant positive regulatory effects. 3) The marketization of agricultural factors impacted the green production efficiency of agriculture by optimizing the factor endowment structure. The mediating effects of endowment structures of land factors and labor factors were significantly negative, whereas that of capital factors was significantly positive. This means that the factor endowment input had gradually changed from land- and labor-intensive to capital-intensive. 4) The impact of the marketization of agricultural factors on agricultural green production efficiency was regionally heterogeneous, and the impact in the eastern region was significantly higher than that in the central and western regions. 5) The impact of the marketization of agricultural factors on agricultural green production efficiency had a spatial spillover effect. Therefore, the following policy suggestions were proposed: First, the market-oriented reform of agricultural factors should be deepened, and the efficiency of the allocation of production factors should be improved. Second, the intensity of environmental regulations in the agricultural sector should be strengthened 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 create factor inputs based on price signals. Fourth, the differentiated development among regions should be much accounted: the eastern region should further promote the market-oriented reform of factors, and the central and western regions should 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 among regions and promote cross-regional flow of production factors.