The invention belongs to the technical field of bioengineering, and particularly provides an efficient biological desulphurization fungicide and an application method thereof. The involved biologicaldesulphurization fungicide consists of pichia pastoris and candida tropicalis, wherein the accession number of the pichia pastoris is CGMCC No. 16155; and the accession number of the candida tropicalis is CGMCC No. 16156. The fungicide can be applied to treatment of gas containing sulfuretted hydrogen and sulfur-containing wastewater, except for reduction of emission of the sulfuretted hydrogen and the like, biological sulfur can further be recycled, and thus, the economic benefit and the benefit of environmental protection are remarkable.