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Aiming to solve waterlogging stress, an obstacle that limits agricultural production under rain-shelter cultivation in southern China, and quantitatively evaluate the possible influences of biochar on alleviating damage to crops caused by waterlogging stress, tomato was taken as the experimental object, and the effects of different groundwater tables and biochar application rates on water consumption, soil redox potential and yield were analyzed systematically by soil column experiments. The results showed that the shallower the groundwater table was, the more serious the influence of waterlogging stress on tomato was, leading to less water consumption. The total water requirement was significantly reduced with biochar application. However, the soil water kept by biochar was weakened with the decrease of groundwater table. The groundwater recharge was decreased with the increase of groundwater depth. Under the same groundwater table, the application of biochar could significantly increase the contribution of groundwater to water consumption. Biochar application could increase the soil redox potential and improve the ventilation performance of soil. When the groundwater table was -80cm, 5% biochar addition could significantly improve tomato yield and water use efficiency, with an increase of 38.7% and 56.6%, respectively. Groundwater table significantly affected tomato yield, but the interaction of groundwater table and biochar had no significant effect on yield and water use efficiency.