In recent years, China's policies and regulations on ecological environment construction have been improved, and the capital investment has also been increased. However, audit is needed to verify and evaluate whether these policies and regulations are implemented, whether funds are reasonably used, and whether corresponding governance results are obtained. Taking the water environment governance of Chaohu Lake basin as an example, the study uses PSR model, analytic hierarchy process and environment merit model to realize the authentication and evaluation of water environment governance activities in Chaohu Lake basin. The study found that the water environment governance in Chaohu Lake basin has achieved certain results, but with the continuous progress of governance, relevant departments need to clarify their own responsibilities, promote the implementation of governance policies, and promote the establishment and implementation of accountability mechanism, so as to further improve the governance effect. This paper successfully constructed an evaluation index system for water environment performance audit in Chaohu Lake basin, which enriched the research on the evaluation index system of water environment performance audit and provided reference for other areas to carry out water environment performance audit.