Abstract: The river channel section of the south channel of the Yangtze River estuary changed alternately in “U” and “W” shapes from 1958 to 2010. Based on the two-dimensional tidal current mathematical model, the hydrodynamic changes under the topographic conditions of the Yangtze River estuary in 1958, 1973, 1997 and 2010 are respectively simulated, and the impacts of topographic changes on the tidal wave transmission and tidal current movement are analyzed. The research results show that the hydrodynamics in the study area (south channel) is closely related to the topographic variation. The tidal range of the south channel reach has gradually decreased, and the tidal wave deformation has gradually intensified since 1958. The tidal current movement is closely related to the development of the Ruifeng shoal. In 1997 when Ruifeng shoal was the largest, the flow velocity of the south channel was distributed in a double pattern. The Changxing waterway was dominated by the high tide, while the other years were dominated by the ebb tide, and the main channel of the south channel was always dominated by the ebb tide. From 1958 to 1973, the diversion ratio of the ebb tide in the south channel decreased significantly, and stablilized after 1973 to about 50%, with little change with the topography.