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The study of aerated irrigation (AI) in conjunction with different irrigation levels on economic and environmental effects has important scientific significance for the selection of optimal irrigation and reasonable greenhouse management practices. In this paper, a two-year experiment was conducted to investigate tomato yield, water use efficiency (WUE), CO2, N2O, CH4 emissions, net global warming potential (NGWP), and carbon footprint (CF) differences for a greenhouse tomato system in Northwestern China in 2016 and 2017. Based on the amount of irrigation needed to provide an adequate water supply (W), 60%W, 80%W and 100%W were set as the three irrigation levels, with two aeration regimes (aeration and control), totaling six treatments. Compared to the control, AI significantly increased tomato yield by 32.0%, WUE by 32.0% and CF by 24.0% on average (p < 0.05), but had no significant effect on soil CO2, N2O, CH4 emissions and NGWP (p > 0.05). With respect to the treatment of 100%W, 80%W over the two years had no obvious effect on tomato yield, WUE and CF (p > 0.05), while 60%W reduced yield by 23.4% and CF by 32.6% but increased WUE by 35.1% significantly (p < 0.05). The effect of different irrigation levels on soil CO2, N2O and CH4 emissions, NGWP in 2017 and CF was not significant (p > 0.05). The main inputs in this arid and semi-arid region were electricity for irrigation and fertilizers, contributing 87.9%-92.9% of the total impact. Overall, the treatment of aerated full irrigation was suitable for crop production, water saving and carbon sequestration with WUE of 24.05 (in 2016) and 19.95 kg m(-3) (in 2017), a net greenhouse gas intensity of 0.103 (in 2016) and 0.086 (in 2017) t t(-1), and with a carbon footprint per tomato yield of 0.350 (in 2016) and 0.426 (in 2017) kg CO2-eq kg(-1).