In the new era, the needs to satisfy people's good life are inseparable from high quality and clean agricultural products. The problem of agricultural pollution not only threatens food safety, but also go against the green transformation of agriculture. From the perspective of interest analysis of political economics, this paper makes a theoretical analysis and empirical research on the problem of agricultural pollution. The results show that firstly there is a competitive relationship between economic interests and environmental interests in the short term. The urgent demand for economic interests of farmers decides that they prefer the former. Secondly, the irrational incentive mechanism of local governments encourages the behavior, and aggravates the pollution degree of agriculture. Thirdly, effective institutional arrangements constrain the boundaries of people's behavior choices, and can effectively reduce the level of agricultural pollution. In addition, the paper further analyzes the regional heterogeneity of agricultural pollution. The prevention and control of agricultural pollution should be integrated with the relationship between economic interests and environmental benefits, perfect the corresponding institutional arrangements and supervision mechanism, design a comprehensive system of political performance assessment and diversified financial agricultural-support methods.