A synchronized method of photon detection array signal slot based on measurement of photon arrival time is proposed. Firstly, to obtain the offset of the arrival time of each photon relative to the position of the pulse position modulation slot, we measure the arrival time of different photons in each branch, and finally the photon distribution at different offsets is obtained statistically. In the presence of frequency offset, the photon distribution becomes much flatter. When the initial phase shift exists, the peak of the photon distribution can deviate from the center position. Then the mean square error or second moment is used as the standard of the synchronization under different frequency offsets and initial phase offsets, and the searching method is used to achieve the slot synchronization. The simulation results show that the proposed method can achieve the slot synchronization when the counting clock frequency is twice or more than the slot clock frequency.