The invention provides an optically pumped magnetometer closed-loop control method based on phase-locked loop fragmentation PID. According to the method, a demodulator, a summator, a comparator, a ANDgate, a PID unit and a digital control oscillator are included. The demodulator comprises a multiplier, a low pass filter, a polar coordinate transformer and a phase shifter, and the demodulator hasthe combined action that an input signal and an output frequency signal of an optically pumped magnetometer are analyzed and compared, and error phase signals are output; the summator overlays the phase signals and the set phase, and signals to be controlled are output; one one hand, the digital control oscillator is controlled by PID for generating a final frequency signal to be shifted, and after the output and the set clinic value are compared, different PID parameter channels are controlled by output of the summator jointly to be connected or disconnected. By adopting the method, the problem that due to the fact that the input signal range is quite large, one set of PID parameters cannot stably control the system can be solved, the working range of the optically pumped magnetometer isenlarged, the optically pumped magnetometer can normally work under different magnetic fields to be measured, and the high control precision and stability are kept.