As the phase of X-ray pulsar signal is hard to obtain accurately because of low signal noise ratio, a method of estimation based on Wavelet-Fisz transformation for X-ray pulsar signal was proposed. The signal of X-ray pulsars were folded by an enormous number of photon events. The signal model of X-ray pulsar was constructed. The Wavelet-Fisz transformation was derived. The signal of X-ray pulsars were preprocessed to Gaussian distribution by Wavelet-Fisz transformation, then the approximated signal was estimated. Several observation data of RXTE were analyzed, the results show the proposed method has a good performance of estimation, with low overhead of time under Wavelet-Fisz transformation, and is suitable for engineering application of X-ray pulsar navigation.