In order to solve the problem that the impulse interference near the service frequency band of aviation radio navigation affects the receiver, and further improve the anti-jamming ability of GNSS system, a impulse interference suppression method based on STFRFT (short time fractional Fourier transform) was proposed. The optimal rotation order of the received signal was determined, and STFRFT was applied to the signal to obtain the two-dimensional distribution of time-frequency surface through coordinate rotation. Under the optimal order, the adaptive time-varying filter was used to separate the interference and the signal, so as to suppress the interference. The simulation results show that the adaptive filtering algorithm based on STFRFT has the best effect of eliminating interference compared with several traditional methods, and retains more useful signals while suppressing impulse interference. By combining STFRFT and adaptive time-varying filtering technology, the ability of suppressing impulse interference is improved, which provides some reference for the impulse anti-jamming technology of aviation radio navigation service.