Excess of water irrigation and fertilizer consumption by crops has resulted in high soil nitrogen (N) losses and underground water contamination not only in China but worldwide. This study explored the effects of soil N input, soil N output, as well as the effect of different irrigation and N- fertilizer managements on residual N. For this, two consecutive years of winter wheat (Triticum aestivum L.) -summer maize (Zea mays L.) rotation was conducted with: N applied at 0 kg N ha yr , 420 kg N ha yr and 600 kg N ha yr under fertigation (DN0, DN420, DN600), and N applied at 0 kg N ha yr and 600 kg N ha yr under flood irrigation (FN0, FN600). The results demonstrated that low irrigation water consumption resulted in a 57.2% lower of irrigation-N input (p <0.05) in DN600 when compared to FN600, especially in a rainy year like 2015-2016. For N output, no significant difference was found with all N treatments. Soil gaseous N losses were highly correlated with fertilization (p <0.001) and were reduced by 23.6%-41.7% when fertilizer N was decreased by 30%. Soil N leaching was highly affected by irrigation and a higher reduction was observed under saving irrigation (reduced by 33.9%-57.3%) than under optimized fertilization (reduced by 23.6%-50.7%). The net N surplus was significantly increased with N application rate but was not affected by irrigation treatments. Under the same N level (600 kg N ha yr ), fertigation increased the Total Nitrogen (TN) stock by 17.5% (0-100 cm) as compared to flood irrigation. These results highlighted the importance to further reduction of soil N losses under optimized fertilization and irrigation combined with N stabilizers or balanced- N fertilization for future agriculture development. [Abstract copyright: Copyright © 2021 Elsevier Ltd. All rights reserved.]