The Changjiang River (CR) is divided into a southern branch (SB) and a northern branche (NB) by Chongming Island as the river enters the East China Sea. Observations reveal that during the dry season the saltwater in the inner shelf of the East China Sea flows into the CR through the NB and forms an isolated mass of saltwater in the upstream area of the SB. The physical mechanism causing this saltwater intrusion has been studied using the high-resolution unstructured-grid Finite-Volume Coastal Ocean Model (FVCOM). The results suggest that the intrusion is caused by a complex nonlinear interaction process in relation to the freshwater flux upstream, tidal currents, mixing, wind, and the salt distribution in the inner shelf of the East China Sea. The tidal rectification, resulting from the interaction of the convergence or divergence of tidal momentum flux and bottom friction over abrupt topography, produces a net upstreamward volume flux from NB to SB. With river discharge the net water transport in the NB is driven through a momentum balance of surface elevation gradient forcing, horizontal advection, and vertical diffusion. In the dry season, reducing the surface elevation gradient forcing makes tidal rectification a key process favorable for the saltwater intrusion. A northerly wind tends to enhance the saltwater intrusion by reducing the seaward surface elevation gradient forcing rather than either the baroclinic pressure gradient forcing or the wind-driven Ekman transport. A convergence experiment suggests that high grid resolution (?100 m or less) is required to correctly resolve the net water transport through the NB, particularly in the narrow channel on the northern coast of Chongming Island.