Two kinds of matching methods of low order equivalent system were studied based on time-domain data. First of all, two source of time-domain data were described and correction formula for the key data of flight test were given. Then, flight simulation of a specific aircraft was conducted using two types of control inputs. The simulation data were used for equivalent matching. The short period mode results of matching coincide with those of theoretical data. Besides, the simulation results of low order equivalent system quite match original time-domain data. These indicated the matching methods were workable and valuable. Finally, according to the influence of control inputs on matching results, some suggestions of how to choose control inputs were given.