In China’s Yangtze River Basin, systematic waterway improvement and dredging maintenance have increased the waterway water depth compared with that before the implementation of the Three Gorges Project. Although the water depth of the middle section increased from 2.9 m in 2002 to 4.2 m in 2021, it remains less than 6.0 m in the lower section and 4.5 m in the Three Gorges Reservoir area. This study explores the Chenglingji—Wuhan reaches in the middle section of the Yangtze River, using hydrological data from 1954 to 2021 and topographic data from 2002 to 2021 to analyze river channel scouring or deposition characteristics, verify the waterway scale with a multi-scale width of 4.5 m water depth, and propose waterway management countermeasures. After the implementation of the Three Gorges Project, the Chenglingji—Wuhan reaches were scouring using a low-flow channel (94.95%), thereby facilitating waterway depth improvement. A serious obstruction area was located in the branching channel, and an unstable relationship between the boundary of the continental bank and the branching channel was found to be the main factor hindering navigation, with a water depth below 4.5 m. The Chenglingji—Wuhan reaches waterway water depth has been raised from 2.9 m in 2003 to 4.2 m; it can be raised to 4.5 m through waterway scale improvement. This study explains the navigation obstruction characteristics of alluvial waterways, which has important reference value for waterway scale improvement and planning, and the efficient utilization of deep-water resources.