Flooding stress constitutes a major abiotic challenge in agricultural production. Flooding stress, including waterlogging and submergence, inhibits plant growth and development through hypoxia, ion toxicity, and energy deficits. As such, plants have evolved various adaptive responses and mechanisms to counter flooding stress under diverse ecological conditions. This review discusses the detrimental effects of flooding stress on plants, as well as the morphological diversity and molecular mechanisms associated with plant adaptation to flooding stress. The genetic strategies for improving plant resistance to flooding stress are also discussed. This review aims to provide guidance for future research into the mechanisms of plant resistance to flooding stress and flooding stress-resistant crop breeding.