In the wheat-maize rotation cultivation system in northern China, excessive irrigation and over-fertilization have depleted groundwater and increased nitrogen (N) losses. These problems can be addressed by optimized N fertilization and water-saving irrigation. We evaluated the effects of these practices on greenhouse gas emissions (GHG), net profit, and soil carbon (C) sequestration. We conducted a field experiment with flood irrigation (FN0, 0 kg N ha yr , FN600, 600 kg N ha yr ) and drip fertigation treatments (DN0, 0 kg N ha yr ; DN420, 420 kg N ha yr ; DN600, 600 kg N ha yr ) in 2015-2017. Compared with FN600, DN600 decreased direct GHGs (N O + CH ) emissions by 21%, and increased the net GHG balance, GHG intensity, irrigation water-use efficiency (IWUE), and soil organic C content (ΔSOC) by 13%, 12%, 88%, and 89.8%, respectively. Higher costs in DN600 (for electricity, labour, polyethylene) led to a 33.8% lower net profit than in FN600. Compared with FN600, DN420 reduced N and irrigation water by 30% and 46%, respectively, which increased partial factor productivity and IWUE (by 49% and 94%, respectively), but DN420 did not affect GHG mitigation or net profit. Because lower profit is the key factor limiting the technical extension of fertigation, financial subsidies should be made available for farmers to install fertigation technology.