Numerous research efforts have been devoted to understanding estuarine morphodynamics under tidal forcing. However, the impact of river discharge on estuarine morphodynamics is insufficiently examined. Inspired by the Yangtze Estuary, this work explores the morphodynamic impact of river discharge in a 560 km long tidal basin based on a 1-D model (Delft3D). The model considers total load sediment transport and employs a morphodynamic updating scheme to achieve long-term morphodynamic evolution. We analyze the role of Stokes drift, tidal asymmetry, and river discharge in generating tidal residual sediment transport. Model results suggest that morphodynamic equilibrium is approached within millennia by vanishing spatial gradients of tidal residual sediment transport. We find that the interaction between ebb-directed Stokes return flow/river flow with tides is an important mechanism that flushes river-supplied sediment seaward. Increasing river discharge does not induce continuously eroded or accreted equilibrium bed profiles because of the balance between riverine sediment supply and sediment flushing to the sea. An intermediate threshold river discharge can be defined which leads to a deepest equilibrium bed profile. As a result, the shape (concavity or convexity) of the equilibrium bed profiles will adapt with the magnitude of river discharge. Overall, this study reveals the significant role of river discharge in controlling estuarine morphodynamics by supplying sediment and reinforcing ebb-directed residual sediment transport.