Agricultural pollution source as Nitrous oxide (N2O) emission from irrigated paddy field as affected by overuse of chemical fertilizer application and flooding irrigation is the primary anthropogenic source of nitrogen (N) losses in the Ningxia irrigation district. The emissions variation and driving factors of N2O emission in the large irrigation districts needs much more investigation. A static chamber-gas chromatograph method was conducted to quantify N losses from a paddy field in Lingwu Farm during 2009–2010. Three nitrogen (N) treatments were conducted, including the conventional N application rate of 300 kg ha−1 (N300), the reducing N application rate of 240 kg ha−1 (N240) and control plot (N0). The N2O emissions due to combined effects of the fertilizer application and flood irrigation after winter dry follow was 2.86–3.27 kg ha−1 in N300. The flood irrigation at the beginning of the rice transplanting promotes N2O emissions due to nitrification–denitrification of a richer N source provided by the N fertilizer accumulation of soil NH4+ and NO3-. During the rice growth stage when the paddy field was submerged, N2O emission was very low while intermittent irrigation before tillering and the maturation stages, frequent alteration of dry and wet soil condition enhance N2O emission. The reducing N fertilizer application improved the recovery rate in rice and resulted in a less N2O emission from irrigated paddy field in the arid and semiarid region while keeping the rice yield.