The performance audit of special funds is an audit method for funds with special designated purposes or special purposes in China’s administrative institutions. In order to better standardize the use of special funds and improve the efficiency of capital expenditure, this paper proposes a complete set of performance audit evaluation index system of special funds, and uses the analytic hierarchy process to calculate the weight of each performance evaluation index, and converts the subjective expert scores into objective quantitative indicators, so as to provide an objective basis for the performance evaluation of special funds and guide the audit practice.