X-ray pulsar navigation technology uses pulsars as navigation beacons, and multiple pulsars with orderly distribution in space are selected to form a function similar to the existing navigation satellite network. X-ray detectors receive highly stable pulse signals emitted by distant pulsars, record photon arrival time, and then determine the position, attitude, speed and time of spacecraft through algorithms to provide navigation information for spacecraft and realize autonomous navigation. Accurate measurement of photon arrival time is a very important part of X-ray pulsar navigation, and photon arrival time accuracy is an important factor affecting the navigation accuracy. Therefore, a measuring system for photon arrival time accuracy of X-ray detector is established. The system mainly consisted of pulse X-ray generator, arbitrary waveform generator, Avalanche Photodiode (APD) and time-marked photon counter. The pulse X-ray generator consists of X-ray modulation tube and high-voltage and control circuit. In the X-ray modulation tube, the cathode filament is energized and heated to release electrons, which are accelerated at high anode pressure, the modulating electrode adjusts the number of electrons passing through, the focusing pole focuses the electron beam, and finally the electron beam hits the anode target to produce X-rays. Among them, the electric field formed by the modulating pole voltage is equivalent to the external electric field of the hot cathode. When the modulator voltage is negative, the electron beam can be blocked from passing through the modulator. After the negative voltage gradually increases, the electron beam is completely blocked and cannot stimulate the X-ray. This voltage is the cut-off voltage, which is -3 V after test. The arbitrary waveform generator generates a pulse control signal to control the modulation pole of the X-ray modulation tube. When an arbitrary waveform generator controls the pulse X-ray generator to simulate the pulsar signal, the control pulse with corresponding pulse profile can be generated. In this experiment, in order to simplify the experiment, the function of arbitrary waveform generator is replaced by a signal generator, and the pulse control signal is set as a narrow pulse varying from -3 V to 1 V, with a pulse width of 25 ns. When the modulation pole voltage is 1 V, the pulse X-ray generator can normally emit X-ray photons. When the modulation pole voltage is -3 V, no X-ray photon is produced. The narrow pulse waveform is designed to ensure that only one photon or a certain probability of no photon is generated in an X-ray modulation tube in a pulse period, so as to avoid the occurrence of multiple photons and reduce the error interference. At the same time, the narrow pulse can also ensure that the X-ray photons can be concentrated at the same time during the very short time when the X-ray modulation tube is on, so as to avoid the scattering of photon emission time. The APD detector receives the X-ray photon signal, each photon received generates a negative pulse with a pulse width of about 20 ns and a signal amplitude of about 150 mV, and the output pulse is connected to the time-marked photon counter. The time-marked photon counter measures the time delay between the control pulse signal generated by the arbitrary waveform generator and the measured output signal of the APD detector. Then the distribution of delay is studied, and the results show that compared with the control signal, the time delay of the APD output signal is about 9.03 ns, and the standard deviation is 2.23 ns, that is, the photon arrival time precision of the APD is 2.23 ns. The results show that the APD can realize the fast time response and high precision labeling of the single X-ray photon.