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Nano-bubble irrigation, as a new irrigation technology, can deliver fertilizer-mixed oxygen-enriched water to the root zone of crops, representing a new means for increasing crop yield and carbon sequestration and emission reduction. To systematically analyze the effects of nano-bubble irrigation on crop yield, soil aeration, and soil greenhouse gas (GHG) emissions, as well as evaluating its contribution to the net greenhouse warming potential (<i>NGWP</i>) in greenhouse agriculture, this study was conducted in greenhouse facilities in Zhengzhou, China and focused on tomato plants. A 2-factor, 2-level, completely randomized trial of nitrogen application (low N₁: 120 kg/hm² and normal N₂: 180 kg/hm²), conventional irrigation, and nano-bubble irrigation (C: 5 ppm and A: 15 ppm) was conducted. Compared with conventional irrigation, crop yield increased by 18.94% and 16.36% (<i>p</i> < 0.05), CO₂ emission by 10.72% and 5.71% (<i>p</i> < 0.05), N₂O emission by 29.76% and 35.74% (<i>p</i> < 0.05), and CH₄ uptake by 300.67% and 327.67% (<i>p</i> < 0.05) under nano-bubble irrigation. The nano-bubble irrigation increased the crop yield, thus significantly improving the NGWP sink for greenhouse gases. The low-nitrogen and regular-nitrogen treatments increased NGWP by 22.69% and 14.52%, respectively (<i>p</i> < 0.05). This suggests that nano-bubble irrigation can significantly improve soil aeration, increase tomato yield and biomass, and significantly improve crop carbon sequestration. In the future, nano-bubble irrigation can be used along with soil amendments to achieve a more efficient increase in yield and enhance the ability of farmland to sequester carbon and reduce emissions.