The invention discloses a three-optical-path signal compensation system in an optical MEMS accelerometer and a method thereof. The three-optical-path signal compensation system comprises a three-optical-path compensation optical path and a signal processing system, wherein the three-optical-path compensation optical path comprises an optical isolator, a miniature beam splitter prism, a plane mirror, an adjustable attenuator and an photoelectric detector; and the compensation signal processing system comprises three analog-to-digital (AD) conversion modules, a subtracter, a divider, a data storage, summation and average module and multiplier, and the modules are realized through a programmable digital signal processor. The three-optical-path signal compensation system is relatively simple in structure, and can effectively reduce influences imposed on output signals by power fluctuation of a light source and ambient light. Compared with a scheme of adopting a laser with extremely high power stability, the cost of the optical MEMS accelerometer can be effectively reduced. In addition, the system and the method disclosed by the invention can be effectively applied to the optical MEMS accelerometer, disturbance of the output signals is reduced, and finally the zero-bias stability and the precision of accelerometer measurement are improved.