In this paper, we propose a high fidelity phase-sensitive optical time-domain reflectometer (Ф-OTDR) system based on compact and flexible multi-frequency probe pulse modulation. Single-frequency continuous light is multi-frequency modulated by a broadband acousto-optic modulator (AOM) loaded with multiple microwave signals of different frequencies, finally, multiple Rayleigh backscattered (RBS) optical signals with different intensity distributions can be obtained by a single acquisition, and the most accurate signal is always selected for phase reconstruction to achieve the high fidelity Ф-OTDR system, which has the advantages of compact structure, precise control of phase delay, flexible and controllable frequency components, and no sacrificing response bandwidth and spatial resolution, etc. In the experiment Ф-OTDR system, we simultaneously modulate the multi-frequency probe pulse light with a width of 100ns and three non-equidistant frequencies, and inject it into a 2km sensing fiber. The RBS light signal multiplexing results show that the probability of interference fading effect in the system is reduced from 17.541% to 1.123%. And the highfidelity phase information of a 100Hz simulated vibration signal was extracted on a 3km sensing fiber, corresponding to a strain value of about 11.9nε. Distributed optical fiber sensing, phase-sensitive optical time domain reflectometer, interference fading effect.