The equivalent system method is one of the important methods for evaluating the flight quality of aircraft. The least square method and the maximum likelihood method are widely applied in the formulation of equivalent systems, but both of them require highly of the initial value and are easy to fall into a local optimal solution leading the fitting accuracy to be low. In view of the abovementioned facts, the core formula of traditional differential evolution algorithm is improved, and a new idea of equivalent system fitting based on average differential evolution algorithm is proposed. In addition, because there is a certain percentage of noise interference in the data, the ideal 3211 signal and the 3211 signal mixed with 10% and 30% white noise are used as system inputs, respectively. The difference between the differential evolution algorithm and the traditional equivalent matching method is studied, and the results show that the average differential evolution algorithm has a strong antinoise interference ability, good robustness, good identification effect, and at the same time the processing ability of noise is strong.