Phase sensitive optical time-domain reflectometry system due to its advantages of distributed optical fiber sensing technology has a high application prospect in low frequency monitoring fields such as distributed hydrophone, fracture micro-seismic detection and natural disaster warning. The problem of different clock source of pulse chopper signal and frequency modulated signal in the system was verified and the influence was analyzed theoretically in this paper. A dual-channel synchronous clock source was designed to generate pulse chopper signal and frequency modulation signal to reduce the random low-frequency phase noise of frequency modulation signal in each pulse repetition period and improve the phase stability of the detection pulse light. The acousti-optic modulator of typical phase-sensitive optical time-domain reflectometry system based on heterodyne coherent detection was driven by clock homology and clock non-homology, a signal generator drives a piezoelectric ceramic wrapped in optical fibers to generate disturbance signals in different frequency bands. The experimental results show that under the same test conditions, the former is superior to the latter in the aspects of SNR, phase demodulation quality and frequency response in low frequency band. The minimum response frequency is 0.1 Hz, which is 2 orders of magnitude higher than the latter, and reduces the interference of low frequency noise in the system. The method was easy to implement and compatible with the existing low frequency performance optimization methods or structures to further improve the low frequency response performance of the system.