The invention discloses a spray evaporation treatment method and system for a desulfurization wastewater flue. The system comprises a smoke treatment system, a desulfurization wastewater spray evaporation system, a bypass flue system and an automatic control system, wherein the smoke treatment system comprises an air preheater, a flue, a demister, a dust remover, a desulfurization tower and a chimney; the desulfurization wastewater spray evaporation system comprises a settling tank, a water storage tank, a water pump, a heat exchanger and a spraying device; the bypass flue system comprises a bypass flue 1 and a bypass flue 2; the automatic control system comprises an actuator, a smoke acid dew-point instrument and a controller. A smoke inlet is formed in the wall surface of a flue of the desulfurization wastewater spray evaporation system, and an airflow protection layer is formed, so that the corrosion caused due to the splashing of acidic drops to the wall surface is prevented, meanwhile, the turbulence flow degree of a space is increased, and the evaporation is accelerated. The system is easy to process and manufacture, and low in investment cost, and the evaporation efficiency is greatly improved.