Abstract: Affected by economic and social activities, the Yangtze River Basin confronts problems including resource shortage, frequent pollution and water and soil loss. The protection of water resources and the ecological environment urgently requires solutions. Based on the theories of Dualistic Water Cycle, Land-Sea Integration and overall governance of water resources, water environment and water ecology (“Three Waters Overall Planning”), the evaluation index system of “Three Waters Overall Planning” is constructed and composed of 5 subsystems: the sustainability system, barrier system, conservation system, economic system and social system. The entropy weight TOPSIS model and the obstacle degree model are applied to analyze the spatiotemporal variations and influencing factors of the performance of “Three Waters Overall Planning” in 25 prefecture-level and above cities within the middle and lower reaches of the Yangtze River from 2008 to 2023. The results show as follows: (1) The average score of “Three Waters Overall Planning” performance in the middle and lower reaches of the Yangtze River is 0.1624, ranking at the upper-medium level. Among them, the average score of the middle reaches is 0.1743, and the governance performance is slightly better than the average score of 0.1557 in the lower reaches, but there are significant spatiotemporal disparities. (2) In the middle and lower reaches of the Yangtze River, the average annual growth rate of “Three Waters Overall Planning” performance is generally positive, and the coefficient of range is also relatively stable. The overall level of governance performance showed a continuous upward trend. Among them, the governance performance score of Shanghai consistently remained at a relatively high level for a long time during the research period, with outstanding achievements, while Jiujiang, Ma’anshan, Hefei and Nanchang exhibited a fluctuating downward trend. (3) The obstacle degrees of the main factors affecting the management of “Three Waters Overall Planning” in the middle and lower reaches of the Yangtze River is conservation system > social system > barrier system > economic system > sustainability system, and the obstacle factors are different among cities. To determine the governance priorities for different regions, it proposes countermeasures such as restoring natural barriers, improving top-level design, and developing cloud-based management, providing references for water resource management, water ecological environment protection, and sustainable development in the middle and lower reaches of the Yangtze River.