The invention belongs to the biotechnical field of environment, and concretely relates to a clean flue gas bio-desulfurization and denitrification method and an apparatus thereof. Four bio-reactions comprising denitrification, sulfate reduction, methane production and sulfur oxidation elemental sulfur production and sulfide stripping/hydrogen sulfide absorption combination are adopted to collect oxysulfides in flue gas and directly convert the oxysulfides into highly pure sulfur and convert nitrogen oxide into nitrogen; and an absorption liquid can be regenerated, so the consumption of alkalis and water is saved. Solid wastes and wastewater are not generated in the treatment process, and secondary pollution is avoided.