Water-air coupled oxygen supply to the root zone can significantly enhance crop yield and quality under non-waterlogged conditions. However, its impact on crops subjected to waterlogging-induced hypoxia remains unclear. In this study, tomatoes were chosen as the model crop due to their economic value and sensitivity to waterlogged conditions. Two tomato cultivars, "Micro-Tom" and "Omanda-3," were subjected to waterlogging and treated with varying levels of water-air coupled oxygen supply. The results demonstrated that supplying 25 mL or 50 mL of air per plant to the root zone significantly improved biomass compared to waterlogged plants without additional oxygen. Notably, root dry weight increased by over 73.0% in both varieties. Root morphological analysis revealed that oxygen supply in the root zone greatly promoted root growth, with marked increases in surface area (149.7%), root length (181.2%), fork number (198.4%), and tip number (165.4%). Furthermore, photosynthesis and antioxidant assays showed substantial increases in the leaf net photosynthetic rate, transpiration rate, stomatal conductance, as well as catalase and peroxidase activity in response to oxygen supply. Consequently, fruit yield increased by 86.2% in Micro-Tom and 24.3% in Omanda-3. In conclusion, oxygen supplementation through the water-air coupling technique effectively enhanced root growth, photosynthesis, and antioxidant capacity in waterlogged tomato plants, alleviating hypoxic stress and associated yield losses. These findings offer a theoretical basis and practical recommendations for managing waterlogged farmland in diverse agricultural contexts.