The pulse time of arrival (TOA) is a determining parameter for accurate timing and positioning in X-ray pulsar navigation. The pulse TOA can be calculated by comparing the measured arrival time with the predicted arrival time of the X-ray pulse for pulsar. In this study, in order to research the measurement of pulse arrival time, an experimental system is set up. The experimental system comprises a simulator of the X-ray pulsar, an X-ray detector, a time-measurement system, and a data-processing system. An X-ray detector base is proposed on the basis of the micro-channel plate (MCP), which is sensitive to soft X-ray in the 1–10 keV band. The MCP-based detector, the structure and principle of the experimental system, and results of the pulse profile are described in detail. In addition, a discussion of the effects of different X-ray pulse periods and the quantum efficiency of the detector on pulse-profile signal-to-noise ratio (SNR) is presented. Experimental results reveal that the SNR of the measured pulse profile becomes enhanced as the quantum efficiency of the detector increases. The SNR of the pulse profile is higher when the period of the pulse is smaller at the same integral.