The invention relates to a desulfurization system and method for flue gas of a cement kiln furnace. The desulfurization system comprises an ammonia water storing tank, conveying pumps, spraying guns, a cement decomposing furnace, a cement kiln pre-decomposing system and an automatic control system, wherein the cement kiln pre-decomposing system comprises a multi-stage pre-heater; the ammonia water storing tank communicates with the spraying guns through the conveying pumps; and spraying points of the spraying guns are located at an outlet of a cyclone barrel of a second-stage pre-heater. The desulfurization method comprises the following steps of I, preparing a 15-25% ammonia water; II, performing real-time detection on the concentration of SO2, and according to the concentration of the SO2 in flue gas, calculating and adjusting the spraying amount of the ammonia water through the automatic control system; and III, according to the spraying amount of the ammonia water, which is obtained through calculation in the step II, injecting the ammonia water which is pressurized through the conveying pumps to the spraying guns, and spraying the ammonia water into the cement kiln pre-decomposing system, wherein the spraying points of the spraying guns are located at the outlet of the cyclone barrel of the second-stage pre-heater. According to the desulfurization system and method disclosed by the invention, the desulfurization efficiency can reach 95% or above, the desulfurization efficiency is high, the ammonia-sulfur ratio is 2-2.5, and the operating cost is low.