The invention relates to a system and a method for desulfurizing and denitrating flue gas and by-producing nitrophosphate fertilizer by using ground phosphate rock and phosphorous slurry, and belongsto the technical field of resource utilization and environmental protection. The system comprises a spraying tower I, a curing tank I, a circulating pump I, a spraying tower II, a curing tank II, a circulating pump II, a spraying tower III, a curing tank III, a circulating pump III, a slurry storage tank, a disc filter, a filtrate tank, an ammoniation tank, a filter press, a concentrator, a steamexhaust cooler, a condensed water storage tank, a slurry mixing tank, a ground phosphate rock storage tank and a phosphorus slurry storage tank. The ground phosphate rock and the phosphorous slurry are used as desulfurization and denitration agents for desulfurization and denitration treatment on the flue gas to remove SO2 and NO in the flue gas, so that SO2 and NO in the flue gas reach the emission standard, phosphoric acid is subjected to ammoniation by NH4HCO3, ammonium phosphate nitrate fertilizer is obtained, waste water is returned to be used for blending after treatment, and the ammonium phosphate nitrate fertilizer contains quick-acting -NO3<-> and water-soluble P2O5 and long-acting -NH4<+> and citric acid soluble P2O5.