Equivalent system simulation is a method to effectively evaluate the flight quality of highorder fly by wire aircraft. The traditional equivalent matching usually adopts the method of least squares, and the matching result is susceptible to the selection of the initial value. Firstly, a closed loop pilotaircraft system model , in consideration of the dynamics of a certain aircraft, the fly by wire system, the pilots manipulation and elevator,is established, and then an equivalent system matching process based on adaptive clonal selection algorithm is presented.Finally, the closedloop highorder pilotaircraft system is adopted by the adaptive clonal selection algorithm. A low-order equivalent fit is performed, and the accuracy of the fit meets the requirements of the adaptive envelope. The simulation results show that the adaptive clonal selection algorithm has strong ability to optimize, and can be used to effectively improve the accuracy of the proposed matching.