Gaseous nitrogen (N) emissions, especially emissions of dinitrogen (N2) and ammonia (NH3), have long been considered as the major pathways of N loss from flooded rice paddies. However, no studies have simultaneously evaluated the overall response of gaseous N losses to improved N fertilization practices due to the difficulties to directly measure N2 emissions from paddy soils. We simultaneously quantified emissions of N2 (using membrane inlet mass spectrometry), NH3 and nitrous oxide (N2O) from a flooded paddy field in southern China over an entire rice‐growing season. Our field experiment included three treatments: a control treatment (no N addition) and two N fertilizer (220 kg N/ha) application methods, the traditional surface application of N fertilizer and the incorporation of N fertilizer into the soil. Our results show that over the rice‐growing season, the cumulative gaseous N losses from the surface application treatment accounted for 13.5% (N2), 19.1% (NH3), 0.2% (N2O) and 32.8% (total gaseous N loss) of the applied N fertilizer. Compared with the surface application treatment, the incorporation of N fertilizer into the soil decreased the emissions of NH3, N2 and N2O by 14.2%, 13.3% and 42.5%, respectively. Overall, the incorporation of N fertilizer into the soil significantly reduced the total gaseous N loss by 13.8%, improved the fertilizer N use efficiency by 14.4%, increased the rice yield by 13.9% and reduced the gaseous N loss intensity (gaseous N loss/rice yield) by 24.3%. Our results indicate that the incorporation of N fertilizer into the soil is an effective agricultural management practice in ensuring food security and environmental sustainability in flooded paddy ecosystems.