Abstract: A strong correlation exists between the evolution of the point bar and shoal in the fluctuation segment of the tidal current limit in the lower reaches of the Yangtze River, with simultaneous influences from the hydrodynamic force of runoff and tidal currents, sediment sources, and human activities. This segment is crucial to channel regulation and dredging maintenance. Based on analyses of riverbed scouring and silting, branch channel diversion ratio, and evolution of Sanyiqiao point bar and shoal from 1976 to 2017, the driving mechanism of the evolution of this bar and shoal was clarified. Since 2012, at a depth of 12.5 m at the Sanyiqiao point bar, the shoal-body volume has been increasing. During high rainfall years, the point bar was dominated by silting, and the designed and deep channels were dominated by scouring. In medium rainfall years, the thickness of point bar deposition was less than that in the deep channel. Wufengshan bend in the upper reaches showed a stable river regime and had the functions of blocking the river regime of the upstream Hechangzhou River segment and adjusting the branch channel diversion ratio. The relationship between siltation at the Sanyiqiao point bar and the river-regime adjustment and branch channel diversion ratio of the upstream Hechangzhou River segment was not significant. It was mainly related to the scale and process of incoming flow in the river basin as well as scouring in the upstream river segment as sediment source. During the flood season, navigation obstruction in the upper shallow area of Sanyi Bridge was greater than that during the dry season. Navigation obstruction in years with a long duration of intermediate water flow before the flood season was greater than that during the same period in flood years (flow at Datong hydrological station was 26 000—34 000 m³/s). Therefore, the flow determined the scouring and silting distribution at the point bar and shoal, whereas the duration of intermediate water flow and amount of sediment supply determined the siltation volume at the point bar and shoal, respectively, obstructing navigation.