Complex system evaluation lies in the core position of system engineering theory and methodology and is also a research hotspot and difficulty in system engineering theory and practice research. The paper, taking performance evaluation of integrates with agriculture base and supermarket for example, advances an evaluation indicator system and a fuzzy comprehensive evaluation algorithm. Firstly, a performance evaluation indicator system of integrates with agriculture base and supermarket is designed through analyzing the similarities of general performance evaluation and the specialties of the evaluation object; Secondly, the principle of analytic hierarchy process and fuzzy comprehensive evaluation algorithm are analyzed and the two methods are combined to advance a new algorithm to evaluate complex system with dynamics, subjective and transitional evaluation indicators and improve evaluation accuracy; Thirdly, three integrates are taken for experimental examples and the results illustrate that the improved algorithm can be used for evaluating the performance of integrates with agriculture base and supermarket feasibly and effectively and can provide reference for evaluating other complex systems.