The invention provides a method for preparing a nitrogen-phosphorus-kalium compound fertilizer from boiler flue gas and vitriol tail gas. The method comprises the followings steps: the boiler flue gas and vitriol tail gas are sent to a first flue gas desulfurization tower and added with ammonia to generate imide solution containing ammonium bisulfite and ammonium sulfite; the gas is sent to a second flue gas desulfurization tower and is added with ammonia to further perform desulfurization and washing and exhaust the gas; the partial imide solution in the second flue gas desulfurization tower is returned to the first flue gas desulfurization tower for cyclical washing; the partial imide solution in the first flue gas desulfurization tower is sent to a reaction tank and added with phosphoric acid to displace SO2 from the imide solution, and the reaction slime is sent to a SO2 desorption tower to analyze the SO2 by air; the SO2 obtained by displacement and analysis is used to produce vitriol; the vitriol is used to produce the phosphoric acid; the phosphoric acid is sent to the reaction tank for recycling; and the reaction slime in the SO2 desorption tower is finally injected in a nitrogen-phosphorus-kalium compound fertilizer slime tank, evenly mixed with KC1 and conveyed to a slime spraying granulation compound fertilizer producing device to produce the NPK compound fertilizer.