For the deep space optical communication system based on pulse position modulation (PPM) and photon detection array, a PPM slot synchronization method that directly predicted frequency offset and initial phase offset was proposed. In this method, the arrival time of each photons was measured firstly, and in this way, it can get the offset of every photon′s arrival time relative to PPM slot position and draw out the photon distribution diagram of different offsets of the half-frame forward and backward. Then, the frequency offset was evaluated by using the offset of the photon distribution between the half-frame forward and backward(i.e. the cumulative value of frequency offset in the half frame data). After correcting the data of the arrival time of photons according to the frequency estimation value, the initial phase offset can be estimated by calculating the offset between the frequency corrected photon distribution and that of the ideal synchronization. The simulation result shows, when the counting clock frequency in the receiver is equal or greater than 4 times that of the PPM slot, this method can realize PPM slot synchronization.