In recent years, global climate anomalies and frequent flooding disasters have led to large-scale reduction and even crop failures of ginger production, severely restricting the normal production of ginger. However, the mitigation mechanism under waterlogging stress has not been reported in ginger. In order to investigate the physiological mechanism of the mitigation of waterlogging stress in ginger, the experiment was set up by soil application of urea peroxide(UHP) of different concentration (T1: 0 g·L−1; T2: 40 g·L−1; T3: 80 g·L−1; T4:120 g·L−1) after 2 d of waterlogging. The results showed that waterlogging stress significantly increased the accumulation of ROS and membrane lipid peroxidation in ginger roots and leaves. The chlorophyll content and photosynthetic performance were significantly decreased, and the net photosynthetic rate (Pn), Fv/Fm and ΦPSII of T1 were reduced by 123.5%, 18.8%, and 43.4% compared with that of CK, respectively. Exogenous application of UHP significantly improved the growth of ginger seedlings after waterlogging stress. UHP promoted the rapid recovery of ginger seedlings under waterlogging stress by restoring the normal physiological activity of the root system, and the root activity of T3 was significantly increased by 118.9% compared with that of T1. UHP protected the cellular structure of ginger leaves and improved the H2O-CO2 exchange capacity, and the Pn and stomatal conductance (Gs) of T3 were significantly increased by 961% and 21.8% compared with that of T1, respectively. In addition, the Fv/Fm and ΦPSII of T3 were increased by 20.6% and 48.2% compared with that of T1, respectively. UHP also significantly increased the activity of antioxidant enzymes, and the levels of ROS and membrane damage were significantly reduced.