The frequency of waterlogging events is increasing in recent years due to climate change. Wheat, a dryland crop, is particularly sensitive to waterlogging. Moreover, waterlogging stress is especially serious in the main wheat-producing regions at the middle and lower reaches of the Yangtze River as influenced by regional climate, soil, rotating system and other factors. Oxygen content in soil decreases under waterlogging condition, which inhibits root growth, restricts plant growth, and eventually reduces wheat yield and grain quality. In the present study, we reviewed the current national and international research progress in the underlying physiological mechanisms of inhibitory wheat growth by waterlogging stress, from the aspects of root respiration, water transport, mineral nutrient absorption, photosynthesis, redox metabolism. We discussed the physiological adaptions of wheat to waterlogging, including maintaining energy supply through anaerobic respiration and oxygen supply through changes of root morphology. We listed the application of cultivation measures such as fertilizer regulation, growth regulator regulation and stress memory in improving waterlogging stress-tolerance in wheat with the underlying physiological mechanisms summarized. We also prospected the future study on waterlogging stress-tolerance in wheat, aiming to provide theoretical foundation for waterlogging-tolerant cultivation and maintaining high yield of wheat.