The invention discloses an immobilized microorganism reactor and a reuse method thereof. The immobilized microorganism reactor comprises a protective shell, wherein the protective shell is internally provided with an immobilized microorganism layer; the immobilized microorganism layer is internally provided with a buoyancy regulating layer; and a magnetic force layer is arranged in the buoyancy regulating layer. The immobilized microorganism reactor and the reuse method disclosed by the invention have the advantages that the problems of loss, deposition and blocking of fillers or carriers of the immobilized microorganisms are thoroughly solved; the physical damage is reduced, and the service life of the fillers or the carriers of the immobilized microorganisms is prolonged; the applicability to multiple different processes in a sewage plant is achieved, and the modification for the original sewage treatment infrastructure is not needed; the cost is low, and the management is convenient; and the application range is wide, and the immobilized microorganism reactor and the reuse method not only can be used for suspended fillers, embedding microorganism carriers and enzyme preparations, but also can be used for granular sludge or powdery strains, and not only can be used for urban sewage treatment plants, but also can be used for strain management of black and odorous water bodies of rivers in different environments.