In order to improve the fault tolerance capability of the integrated navigation system based on X-ray pulsar navigation(XNAV), the wavelet method was applied to ensure the accuracy and reliability of the integrated navigation system. The integrated navigation system included XNAV subsystem, celestial navigation subsystem and ultraviolet navigation subsystem. The wavelet technique was used to detect the faults of sensors. If there were a fault in a sensor, the fault one would be isolated from the integrated navigation system. The information fusion was conducted by using federated filter. Results of simulation which was conducted in the Mars exploration orbit demonstrate that this proposed method can find the fault time points of sensors successfully. This method can solve the problem of low accuracy, which is caused by the faults of sensors. Meanwhile, this integrated navigation system can achieve high accurate navigation accuracy and improve the fault tolerance capability and the usable value in engineering.