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The reactive nitrogen (N) loss of the rice cropping system in the arid region shows a different pattern from that of subtropical humid region due to different climate types and crop management. However, little attention has been paid to this region. To fill this knowledge gap, a two-year (2009–2010) field observation was conducted in the Ningxia irrigation region, northwest China, to explore the major pathway of N loss following local farmers' optimal practice. Further, we determined the site-specific emission factors of ammonia and nitrous oxide, rate of surface runoff and subsurface (leaching and seepage) to improve the inventory resolution of arid irrigation region. Results showed that ammonia volatilization (45%–49% of total N loss), leaching and seepage (30%–33% of total N loss) were proved to be the primary factors of N loss in rice paddy fields. The emission factor of ammonia (21%) and N leaching rate (7.5%) following farmers' practice were 2.1 and 5.4 times higher than the country-specific default value in China. The country-specific N runoff rate and emission factor of N 2 O could be directly adopted in this region. A 20% reduction of N fertilizer to farmers' practice (300 kg N ha−1) alongside the application of organic fertilizer (30% N in synthetic fertilizer was substituted by pig manure) were considered to be the optimal N rate in this region. Our study can narrow the gap between researches on N loss in arid regions and subtropical humid regions. Meanwhile, the results can provide specific advice on N loss mitigation for policy makers in arid irrigation regions. • NH 3 emission and N leaching are main N loss for rice paddy in arid irrigation area. • NH 3 volatilization rate and N leaching rate were underestimated previously. • 20% N fertilizer reduction reduce environmental loss without yield penalty. [ABSTRACT FROM AUTHOR]