The latest reform of China’s agricultural land property rights system has achieved the separation of rural land ownership, contracting rights, and management rights (the “three rights separation” reform), which is an important means for the Chinese government to achieve the rational allocation of agricultural land resources and plays an important role in improving the green and high-quality development of agriculture. Based on the panel data of 30 sample provinces in China from 2001 to 2020, this paper explores the impact of the latest rural land property rights system reform (the “three rights separation” reform) on the high-quality green development of agriculture. Research has found that, firstly, the reform of the agricultural land property rights system that separates the collective ownership of land, the contracting rights of farmers, and the management rights of land can effectively improve the green development of agriculture. Secondly, the “three rights separation” reform can enhance the green development of agriculture through three paths: expanding the scale of agricultural economy, promoting the upgrading of agricultural industrial structure, and innovating agricultural technology. In addition, fiscal investment in supporting agriculture has played a positive regulatory role in the impact of the “three rights separation” reform on the green development of agriculture. Thirdly, the impact of the “three rights separation” reform on agricultural green development is characterized by regional heterogeneity and production structure heterogeneity, with a more significant promoting effect on the eastern and central regions, as well as the main grain producing areas. The research conclusion provides new ideas for promoting sustainable agricultural development.