At present, agricultural non-point source pollution has become the main source of water pollution, which mainly comes from the excessive use of agricultural chemicals such as pesticides and fertilizers. The TRS is another land system reform in China after the household contract responsibility system, which relaxes the management rights of rural land and clarifies the ownership of land. Using this land reform in China as a case study, this paper constructs panel data for 30 provinces in China to explore the impact of land tenure intensification on agricultural non-point source pollution, using the difference-in-difference (DID) model to identify the causal relationship between the two. The results show that the coefficient of the TRS policy variable is −4.056 at the 1% significance level, indicating that this round of land reform has suppressed agricultural non-point source pollution. The provinces that have implemented TRS have seen an average annual reduction of 405,600 tons in Agnps emissions compared to those that have not implemented TRS, and the scale operation of agriculture and the size of the agricultural economy act as two paths. Moreover, heterogeneity analysis shows that the policy effect of the provinces in non-major food-producing areas is smaller than that of the provinces in major food-producing areas, and the path to realization is also different. Therefore, we should continue to encourage large-scale agricultural operations, cultivate new agricultural business entities, and strengthen the inhibitory effect of TRS on agricultural non-point source pollution.