In order to improve the navigation accuracy of the X-ray pulsar navigation system, in this paper we propose a constant fraction timing method based on the low-pass filter to measure the arrival time of the X-ray pulse in X-ray pulsar navigation. According to the technical scheme, the timing accuracies and dead times of original peaking timing and the improved constant fraction timing are measured. Experimental results indicate that the timing accuracy and the dead time of the peaking timing system are 18 ns and 4750 ns, the timing accuracy and the dead time of the constant fraction timing system are 0.78 ns and 105 ns. The timing accuracy and the dead time of constant fraction timing system are significantly improved compared with those of the peaking timing system. In the X-ray pulsar navigation system, the cumulative pulse profile of the X-ray pulse is constructed in the two different timing systems through measuring the arrival time of the X-ray photon. Experimental results indicate that compared with using the peaking timing system, the cumulative pulse profile of the X-ray pulse using the improved constant fraction timing system is improved obviously, therefore, the navigation accuracy could be improved by using the constant fraction timing system.