The photon detection model of X-ray pulsar and the construction of pulsar integrated pulse profile are discussed. The characteristics of pulse profile which is reconstructed by the way of photon counting are analyzed. A de-noising algorithm based on non-normalized Haar wavelet is proposed, and the optimal parameters for wavelet threshold function are derived based on Haar wavelet. The experimental study is done in the ground simulated experimental system for X-ray pulsar navigation. Experimental results show that the peak signal-to-noise ratio can be improved by at least 2 dB, and the accuracy of time-of-arrival (TOA) measurement is also improved, which is proved by Monte Carlo simulation.