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 (NGWP) 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% (p < 0.05), CO₂ emission by 10.72% and 5.71% (p < 0.05), N₂O emission by 29.76% and 35.74% (p < 0.05), and CH₄ uptake by 300.67% and 327.67% (p < 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 (p < 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.