Frequency control of atomic clocks is a key technology in time keeping. At present, the open-loop control algorithm is mainly used for the frequency control of foreign microwave clocks, but the working principle and performance of domestic optically pumped small cesium clock (hereinafter referred to as domestic clocks) are different from those of foreign atomic clocks of the same type, so the algorithm can not be well adapted to domestic clocks. In order to improve the autonomy and security of the national standard time, based on the noise characteristics of domestic clock, this paper studies the linear quadratic Gaussian control algorithm under the framework of optimal control theory, the algorithm belongs to closed-loop control algorithm, studies the performance of domestic clock from the aspects of synchronization time, frequency control accuracy and frequency control stability, and finally analyzes the influence of different control intervals on the performance of domestic clock. The results show that with the increase of the constraint matrix <i>W<sub>R</sub></i> in the quadratic loss function, the synchronization time increases, the control accuracy decreases, and the control short-term stability increases. When <i>W<sub>R</sub></i> is the same, with the increase of control interval, synchronization time increases, control accuracy decreases, and control short-term stability increases. When <i>W<sub>R</sub></i>=1, synchronization time with control interval of 1 hour is 5 hours, control accuracy is 1.83ns, and Allan deviation of 1 hour is 1.81E-13. When the control interval is 8 hours, the synchronization time is 28 hours, the control accuracy is 4.48ns, and the Allan deviation of 1 hour is 1.48E-13. The medium and long term stability of domestic optically pumped small cesium clock has been improved.