A new method is proposed to assess the flying quality for the aircraft equipped with complex fly-by-wire flight control system. First, the Chirp-Z method is used to convert the time domain signal into frequency domain, and then a method combined with the frequency domain equation error method (EEM) and the output error method (OEM) is used to identify the parameters of low order equivalent system. Finally, the method is applied to a standard example of F-14 aircraft. The results show that the method is correct and has a good identification accuracy in engineering practice.