Atomic magnetometer which uses atoms as sensitive elements have ultra-high precision and has wide applications in scientific researches. The photoelastic modulation method based on photoelastic modulator (PEM) is used in the atomic magnetometer to detect the small optical rotation angle of a linearly polarized light. However, the modulation amplitude of the PEM will drift due to the environmental factors, which reduces the precision and long-term stability of the atomic magnetometer. Consequently, stabilizing the PEM’s modulation amplitude is essential to precision measurement. In this paper, a modulation amplitude stabilization method for PEM based on Field Programmable Gate Array (FPGA) is proposed. The designed control system contains an optical setup and an electrical part. The optical setup is used to measure the PEM’s modulation amplitude. The FPGA chip, with the PID control algorithm implemented in it, is used as the electrical part’s micro controller. The closed loop control method based on the photoelastic modulation detection system can directly measure the PEM’s modulation amplitude in real time, without increasing the additional optical devices. In addition, the operating speed of the modulation amplitude stabilization control system can be greatly improved because of the FPGA’s parallel computing feature, and the PID control algorithm ensures flexibility to meet different needs of the PEM’s modulation amplitude set values. The Modelsim simulation results show the correctness of the PID control algorithm, and the long-term stability of the PEM’s modulation amplitude reaches 0.35% in a 3-hour continuous measurement.