A three-dimension numerical model to simulate the distribution of salt with a mobile boundary in the Yangtze River estuary is established in this paper. The model is based on an international three-dimension coastal ocean circulation model (ECOM model).Some complex topography is taken into account,including the deep waterway and the artificially enclosed tideland. The computed results match well with the observed ones,which imply that the model is capable of describing the temporal and spatial distribution of salt current in the Yangtze River estuary. The model imitates the 3D characteristics of saltwater intrusion,salt in the surface layer is lower and salt in the bottom layer is higher. From measurements during two tidal cycles by this model in February 1-2,7-8,2003,the sectional salt fluxes from the North Branch and the South Branch were calculated. The result shows that salt changes obviously during spring-neap tidal cycle. The sea transports a huge amount of salt into Yangtze River estuary during spring tidal cycle. This research provides the necessary data for prediction of saltwater intrusion and aproposed project for avoiding saltwater intrusion in the Yangtze River estuary.