To solve the problems of fuzziness, nonlinearity and complexity of economic factors and environmental factors in the evaluation of ecological economic benefits of enterprises are studied. Based on the theory of environmental-economic benefits (EEB), this paper defines the value of environmental resources and economic benefits of enterprises, and puts forward the indicators of environmental and economic benefits. The evaluation model of enterprise EEB based on the analytic hierarchy process and fuzzy set algorithm is constructed. By establishing the hierarchical structure model of index system, the intuitive fuzzy judgement matrix is obtained, and the final score of enterprise environmental benefits is calculated by consistency test and weight analysis. After verifying the model, the evaluation method of enterprise EEB proposed in this paper is accurate and reliable, which is helpful to deeply analyse the hidden order and adaptation mechanism of complex adaptation system of enterprise environmental management.