The physical habitat of the middle and lower reaches of the Yangtze River has experienced significant changes after the impoundment of the Three Gorges Reservoir, thereby affecting river functions. Based on data analysis and literature review, this paper examined the alterations in typical physical habitats such as the hydrological condition, river morphology, and vegetation after the TGR operation and their subsequent impacts on flood prevention, navigation, water supply, and typical aquatic organisms. Key areas for further research were identified as follows: 1) monitoring, including systematic and long-term monitoring programs, and the assessment of the effectiveness of river (waterway) management projects and ecological regulation measures; 2) laws and mechanisms of changes in river morphology, vegetation in the main stream and shoals, and the responses and thresholds of flood levels and benthic animals to variations in the physical habitat; 3) methods for predicting medium and long-term trends of hydrological conditions under the influence of multiple factors, channel regulation technologies that adapt to changes in the physical habitat and meet demands, as well as reservoir operation schemes that align with water supply objectives, benthic animal and fish breeding needs. Additionally, integrated research efforts focusing on physical habitat changes, their impacts, and improvement strategies and technologies require increased attention.