The invention provides a biological desulphurization processing reactor, a biological desulphurization processing system, and a processing method. The reactor comprises a three phase separator and a reaction zone. The reaction zone comprises an outer cylinder, a gas guiding cylinder and a lower flow guiding cylinder, such that the reaction zone is separated into an air-lift zone, an anoxic zone, and a descent zone. The three phase separator comprises an outer frustum, an inner inverted frustum, an outer sedimentation tank, an inner sedimentation tank, and an overflow groove, such that the three phase separator is separated into three sedimentation zones. Sulfide-containing wastewater is mixed with oxygen-containing water from the air-lift zone in the anoxic zone; under the effect of immobilized microorganisms, the sulfide is partially oxidized into elementary sulfur; the mixture is delivered through the three phase separator arranged above, such that the immobilized carrier is separated from a water phase and a gas phase, and sulfur particles flow out with water. According to the invention, with the structure of the reactor and the processing method, a good fluidized state is maintained, and the loss of the immobilized carrier is inhibited. The reactor, the system and the method are advantaged in high elementary sulfur production rate, good processing capacity, hydraulic load impact resistance, substrate load impact resistance, simple structure, and easy amplification.