The invention discloses a flue gas denitration system and a denitration process thereof, and belongs to the field of flue gas purification. The flue gas denitration system comprises a coal-fired boiler, a first denitration reaction tower, a dust remover, a second denitration reaction tower and a water circulation device; the first denitration reaction tower is sequentially provided with three denitration reaction layers from top to bottom; the uppermost denitration reaction layer is a SiO2 reaction layer, and is composed of a glass fiber composite layer with a main body of glass fiber; Fe2O3 particles are uniformly distributed in the SiO2 reaction layer; and an NH3 pipeline for introducing gas NH3 is arranged at an inlet of the first denitration reaction tower. The beneficial effects of the invention are that: two-stage denitration process is adopted, the denitration functions of the first denitration reaction tower and the second denitration reaction tower are distinguished; the firstdenitration reaction tower is used for realizing primary coarse denitration treatment on the flue gas aiming at impurities, larger particles and about 50% of NO gas in the flue gas, and the second denitration reaction tower is used for treating finer particles and residual NO and NO2 in the flue gas to remove more than 95% of nitrogen oxides in the flue gas, so that the purpose of deep denitration is achieved.