The high-precision synchronization system is one of the key factors for the accelerator to generate high-quality beams. Based on the existing continuous laser carrier synchronization system of Tsinghua University, this paper analyzes the long-term drift of the reference microwave signal phase difference between different receiving ends, that is, the slow drift of the synchronization system. An electro-optic modulator (EOM) bias voltage control method based on the amplitude of the reference microwave signal at the receiving end was proposed to suppress the slow drift. After adopting this method, the slow drift of the L-band (1300 MHz) synchronization system of Tsinghua University’s VHF band photocathode electron gun test platform was suppressed to 10.45 fs@24 h, and the slow drift of the S-band (2 856 MHz) synchronization system of Tsinghua University’s Thomson Scattering Facility (TTX) was suppressed to 10.53 fs@24 h. Moreover, this method can make the entire synchronization system work in a room temperature environment, effectively improving the adaptability of the synchronization system to the working environment temperature.