In order to solve the problem that the pulse interference near the service frequency band of aviation radio navigation affects the receiver, and further improve the anti-jamming ability of GNSS system, a pulse interference suppression method based on STFRFT(short time fractional Fourier transform) is proposed. This method determines the best rotation order of the received signal, and then STFRFT is 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 is used to separate the interference and signal, and then the interference is suppressed. The simulation results show that the algorithm retains more useful signals and improves the ability of interference suppression.