The invention relates to a deep sea equipment buoyancy regulating system and a working method thereof, and belongs to the field of marine exploration equipment. The system comprises a buoyancy oil bag, an oil outlet normally open type electromagnetic reversing valve, an overflow valve, a hydraulic motor, a throttling valve, an oil outlet normally closed type electromagnetic reversing valve, an oilstorage oil bag, a controller, an oil inlet normally open type electromagnetic reversing valve, a hydraulic pump, a pressure reducing valve, an oil inlet normally closed type electromagnetic reversing valve, a one-way valve, a pressure transmitter and a flow meter, wherein the controller is connected with the flow meter, the pressure transmitter, the oil outlet normally open type electromagneticreversing valve, the overflow valve, the throttling valve, the oil outlet normally closed type electromagnetic reversing valve, the oil inlet normally closed type electromagnetic reversing valve, themotor and the oil inlet normally open type electromagnetic reversing valve through signal lines. According to the system, electric energy can be emitted by utilizing the pressure of seawater, the working state of a reversing valve of a hydraulic system is controlled, the energy consumption in the working process of the deep sea equipment buoyancy regulating system is reduced, and the working timeof deep sea equipment is prolonged.