For a long time, the relationship between agricultural insurance and the input of chemical fertilizer has been controversial. Since the pilot of policy-based agricultural insurance in China, most scholars have only paid attention to the role of the policy in ensuring farmers’ income and reducing farmers’ poverty, but its possible negative impact on the agricultural ecological environment is often ignored. If the pilot of this policy motivates farmers to apply more chemical fertilizers, which in turn causes more serious environmental problems, this would be contrary to the goals of the policy itself. Using the panel data of 31 provinces from 2000 to 2020 in China, this paper regards the pilot of policy-based agricultural insurance as a quasi-natural experiment and uses a difference-in-difference model to evaluate the impact of policy-based agricultural insurance on agricultural fertilizer non-point source pollution. The research results show that the pilot of policy-based agricultural insurance has aggravated the non-point source pollution of agricultural fertilizers in China. After a series of robustness tests, the research conclusion is still valid. At the same time, the effect of policy-based agricultural insurance aggravating agricultural fertilizer non-point source pollution had a lasting impact for 4 years during the pilot period and did not disappear until the policy-based agricultural insurance was fully covered. In addition, the heterogeneity results show that farmers in eastern China and high-disaster areas have a higher probability of moral hazard with overuse after purchasing policy-based agricultural insurance.