The effect of clear water discharge on the river bed evolution of the Yangtze River estuary after the Three Gorges water storage is a common concern of sediment researchers. On the basis of recent changes of sediment and boundary conditions, we analyze the characteristics, morphological evolution and trend of erosion and siltation of the basic channel riverbed in the Yangtze River Estuary. Our findings reveal a comprehensive strong scour of the basic channel of the Yangtze River Estuary. The river bed shape develops toward a smaller width-depth ratio. The erosion distribution of the upper, middle and lower riverbeds in each section reflects that the upstream section of the Yangtze River Estuary is largely affected by runoff, while the downstream is largely affected by tidal energy. The overall river regime of the Yangtze River Estuary will remain relatively stable steadily under the actions of bank protection and recent encirclement projects and shoreline renovation projects. In the presence of a sharp decline of sediment after water storage in the Three Gorges, the basic channel will be continuously scoured, and river bed shape will still develop to be narrower and deeper.