The atomic clock frequency signal link is the most important technology of the atomic frequency standard. This is because of the great difference in frequency between the atomic energy level transition signal and the output signal of the atomic clock. The basic method for the traditional frequency signal processing in phase is limited to the same frequency nominal values. The paper is based on the principle of continuous phase group synchronization and cluster, which makes the phase processing suitable for complex frequency signals. The clock system structure is improved using the methods of the sampling time interval (phase difference) measuring, processing and phase-locked control. Compared with the traditional frequency normalization method, the system frequency change circuit is simplified. By a simple phase lock control of group synchronization, the atomic clock output signal has a good degree of accuracy, a long term stability index, excellent short-term stability and phase noise performance. ©, 2015, Science Press. All right reserved.