The invention relates to a comprehensive treatment method and device for Se-containing wastewater. Two stages of reactors are adopted, the Se-containing wastewater enters a second reactor firstly andis subjected to a reaction with sulfur-containing flue gas, SO2 in the flue gas is removed, and purified gas is discharged; effluent of the second reactor enters an anaerobic reactor, and selenate ions in the wastewater are reduced into selenite ions; effluent of the anaerobic reactor returns to a first reactor and is subjected to a reaction with the flue gas, and the selenite ions are removed; effluent of the first reactor enters an aerobic reactor, and effluent of the aerobic reactor is subjected to flocculating sedimentation, solid-liquid separation is performed, and a product is discharged. The Se-containing wastewater is treated by the sulfur-containing flue gas, so that the Se-containing wastewater and the sulfur-containing flue gas are treated efficiently simultaneously, waste is treated by waste, treatment cost of the Se-containing wastewater is reduced, the removal rate for Se pollutants in the wastewater is higher than 95%, and content of SO2 in the sulfur-containing flue gasis lower than 20 mg/L.