Coherent population trapping (CPT) magnetometer is a new high sensitive atomic optical magneometer for weak magnetic field measurement. According to low phase noise modulated signal requirements in the process of current modulation of vertical cavity surface emitting lasers (VCSEL) of the magnetometer, a scheme based on phase locked loop (PLL) frequency synthesizer is presented. On the basis of basic principles of CPT magnetometer, frequency requirements of modulated signal for CPT magnetometers are analyzed. According to basic principles of frequency synthesis of PLL, key module parameters in frequency synthesizers are determined by ADIsimPLL software. A 3.4 GHz frequency signal with high precision, low phase noise and good spurs is generated and simulation analysis is performed to the system. Simulation results shows that the system has good phase-locking effect, reliable performance and can meet the research of CPT magnetometer.