Abstract: Promoting the green transformation of grain production is of great importance for achieving green agricultural development. Based on panel data from 30 China’s provinces from 2008 to 2023, this study treats the reform of the “separation of three rights” in agricultural land as a quasi-natural experiment and employs continuous difference-in-differences (DID) model to examine the impacts of the reform of agricultural land property rights system on the green total factor productivity of grain production. Results show: 1) the regression results of machine learning indicate that the reform of the “separation of three rights” of agricultural land has a significant positive impact on the green total factor productivity of grain production within the region, although the impact emerges with a time lag. Meanwhile, this conclusion remains robust after a series of robustness checks; 2) the mechanism analysis shows that the reform improves the green total factor productivity by promoting the large-scale agricultural land management and advancing agricultural technology; 3) the heterogeneity analysis reveals that the reform has a stronger impact on the green total factor productivity in major grain-producing areas, regions with high levels of mechanization, regions with more developed new agricultural business entities, and eastern regions of China; and 4) the moderating effect analysis shows that the policy combination of “reform of agricultural land property rights system + high-standard farmland construction” produces a stronger positive effect on the green total factor productivity in grain production. Accordingly, efforts should be made to further promote the reform of agricultural land property rights system, strengthen the research, development, and adoption of green agricultural technologies, and implement differentiated and coordinated reform policies.