Starting from the operational level, taking the classification of natural resources of economic responsibility audit as selection evaluation index, using the analytic hierarchy process (AHP), this paper constructs the judgment matrix, obtains the weight of index and makes the consistency test. On this basis, the overall weight is calculated, a classified design on evaluation index is constructed, thus the initial evaluation index system of economic responsibility audit of natural resources is constructed. What's more, this paper combines the above research methods and results with the method of comprehensive evaluation in order to standardize the management of leading cadres using allocated project funds in national natural resources, so that the economic responsibility of leading cadres to be entrusted with natural resources can be effectively carried out, which provides a scientific and feasible evaluation model for the economic responsibility audit of natural resources in the future.