Abstract: Based on short time Fourier transform(STFT), a study was carried out on longitudinal frequency-domain equivalent matching for time-domain data in flight control system. The input signals of the system were first decomposed by STFT to achieve those signals that most interest the pilots. Then fast Fourier transform(FFT) was used to extract the frequency spectrums of both input and output signals. From the achieved frequency spectrums, the response function was derived and was applied in the low-order equivalent matching to obtain the parameters of low-order system. This method increases the matching efficiency of both high-order and low-order systems, reduces the matching error and improves the evaluation results of flying qualities.