An adaptive method based on wavelet packet transform and TRansform domain Least Mean Square(TRLMS) is proposed in order to solve the problem that the pulse interference near the service frequency band of aeronautical radio navigation affects the receiver, and further improve the ability of pulse interference suppression in the Global Navigation Satellite System(GNSS). By using the best wavelet function decomposition to track the frequency band of the positioning pulse interference, and adopting TRLMS adaptive filtering instead of the conventional fixed threshold method of wavelet packet, the interference is suppressed. The simulation results show that the mean square error of the proposed method is smaller than that of other methods. It solves the problem of useful signal loss and has better interference suppression performance.