The order of modern highly augmented aircraft is very high. It should be reduced to it-s low order equivalent system (LOES) for evaluating the handling quality of aircraft and the design of flight control system. The time-domain equivalent matching can acquire on-line data of input and output, considering the influence of nonlinearities in the system, and the on-line estimation of equivalent parameters is given, it has more practical value than the frequency-domain method. A hybrid optimization algorithm is introduced for the time-domain equivalent matching, namely direct search-simulated annealing method. This method improves the local and global optimization with the limitations to the range of parameters in the process of optimization and can converge the globally optimal solution quickly. The result is not influenced by the initial value and is significant for the on-line evaluation of aircraft handling qualities.