During pulsar navigation, the high-frequency noise carried by the pulsar profile signal reduces the accuracy of the pulse TOA (Time of Arrival) estimation. At present, the main method to remove signal noise by using wavelet transform is to redesign the function of the threshold and level of wavelet transform. However, the signal-to-noise ratio and other indicators of the filtered signal need to be further optimised, so a more appropriate wavelet basis needs to be designed. This paper proposes a wavelet basis design method based on frequency domain analysis to improve the denoising effect of pulsar signals. This method first analyses the pulsar contour signal in the frequency domain and then designs a Crab pulsar wavelet basis (CPn, where n represents the wavelet basis length) based on its frequency domain characteristics. In order to improve the real-time performance of the algorithm, a wavelet lifting scheme is implemented. Through simulation, this method analyses the pulsar contour signal data at home and abroad. Results show the signal-to-noise ratio can be increased by 4 dB, the mean square error is reduced by 61% and the peak error is reduced by 45%. Therefore, this method has better filtering effect.