ABSTRACT With global climate change, waterlogging is occurring with increasing frequency. Waterlogging is an important abiotic stress, which restricts plants growth and development, significantly reduces crop yield and seriously threatens the safety and sustainable development of agricultural production. Therefore, understanding the mechanisms of plant response to waterlogging is essential for the food security. Here, we review the damage of waterlogging, the physiological and morphological adaptation of plants response to waterlogging, summarize the relevant genes and molecular mechanism of plant waterlogging tolerance, and look forward to the current challenges and future directions of cultivating waterlogging‐tolerant varieties. This review provides a scientific basis and research direction for deepening the understanding of plant waterlogging tolerance mechanisms.