Abstract: Policy-based strategic environmental assessment (policy-based SEA) is an important part of the environmental impact assessment system. It is very important to carry out the method research of policy-based SEA for its system improvement and practice. Difference-in-differences (DID) is one of the main methods used to evaluate policy effects in econometrics. Taking the policy of agricultural support and protection subsidy as an example, multi-period DID was used to evaluate the impact of the policy on agricultural non-point source pollution, and explore the applicability of DID in policy-based SEA. This study found that DID had good applicability in policy-based SEA. In addition to the environmental impact assessment of post-implementation policies, DID could also be used for the retrospective evaluation of the relevant policies of pre-implementation policies. In the future, the research on technical methods of policy-based SEA should be strengthened, and a unified technical method system should be formed to promote the construction and improvement of policy-based SEA system. In addition, it was found that although the policy for agricultural support and protection subsidy was a favorable policy for environment, its positive impact on agricultural non-point source pollution was not significant, and even stimulated farmers to use more pesticides, resulting in a negative environmental impact.