Aiming at the pulse position modulation (PPM) system of asynchronous sampling at sampling frequency of 1 slot, we propose a clock synchronization technique based on guard time. One or more guard time are inserted into each PPM signal in the transmitter. Based on the fact that there are only background photons in these guard time, while other slots have the characteristics of both background photons and signal photons, we achieve clock synchronization. At the receiving end, the sampling data is counted periodically with the number of slots in PPM signal. Then, the coarse timing synchronization is carried out based on the statistical distribution characteristics of photon in guard time. Finally, the interpolation matching search method is used for the fine timing synchronization. The simulation results show that the proposed method can achieve efficient synchronization within the scope of large timing offset, and increasing the number of guard time or increasing the amount of statistics can achieve ideal system bit error performance.