A parallel cycle shift comparison method of frame synchronization is designed and implemented. The method is applied to atmospheric laser communication system with transmission rate of 2.5 Gbit·s-1 and pulse position modulation (PPM). The operation principle and the performance of the frame synchronization are studied. The fault-tolerant ability of frame synchronization in atmospheric channel is improved with the special frame head synchronous sequence. The system can maintain high synchronization probability when the channel condition becomes worse with decreasing of the detection threshold. Analysis and simulation results show that the frame synchronization scheme can realize the frame synchronization in the high-speed PPM optical communication, and the detection threshold values are 14, 7-9, 10-13 corresponding to three different atmosphere conditions to maintain good performance of the system.