This article carries on a research on the identification of low order equivalent system dynamic models of fly-by-wire aircraft from flight test data. Frequency domain spectral analysis method is conducted and practical transfer function models are proposed in the article. A frequency domain identification technique is developed by using the output error and equation error parameter identification integrated with Simplex method. The algorithm is validated based on certain aircraft flight test data. The results show good consistency with flight test data and the low order equivalent system identified can properly describe the dynamic response characteristics of fly-by-wire aircraft. This work could provide technique support for flying quality evaluation of fly-by-wire aircraft.