The development of the Yangtze Estuary is impacted by the human interference in the estuary as well as in the river basin. River discharge to the Yangtze Estuary has been changed due to human interference in the Yangtze River Basin. Especially since the construction of the Three Gorges Dam, not only the total annual runoff is decreased, but also the seasonal variation of the discharge is changed. The changed flow regime has caused a significant decrease of sediment input from the Yangtze River to the estuary. These changes together with the large scale engineering works in the estuary itself will inevitably impact the morphological development of the estuary. The aim of our research is to improve our understanding of the morphological development of the Yangtze Estuary and the effect of the human interference by using process-based morphological model. This paper describes the first step of the model set-up, viz. the hydrodynamic modeling of the Estuary. A 2D/3D model is set up for the estuary on the basis of Delft3D. A major improvement with respect to the previous models for the Yangtze Estuary is that the present model covers the entire tidal region of the Yangtze River. As show in figure 1, the upper river boundary of the model is set at Datong, which is tidal limit of the estuary about 640 km far from the river mouth. The sea boundary is set at the depth about 50m with the distance about 160 km from the estuary. In order to cover such a large spatial area, domain decomposition is applied with 2 curvilinear grids. The river domain, also called upper grid, covers from Datong to Jiangyin (the tidal current limit) with 2D coarse grid. The estuary domain, lower grid, consists of the Yangtze Estuary, the Hangzhou Bay and a part of adjacent East China Sea. High resolution is used in the estuary domain with 2D or 3D grid. The observed daily discharge is specified at Datong as boundary condition. This makes it possible to simulate the impact of changes in the upstream, e.g. discharge regime changes. Tidal forcing is provided with tidal constitutes at open sea boundaries. Model results show that the simulated tidal constituents agree well with the tidal analysis results at observation stations. Co-tidal maps show that the semi-diurnal tides propagate from the southeast into the Yangtze Estuary. With the present calibrated and validated model, the influence of discharge regime changes in the upper stream on the Yangtze Estuary is studied at present. Based on this research the morphological evolution in the Yangtze Estuary under influence of sediment load reduction in the upper stream and other human interferences will be further investigated.