At present, the upper reach of the Deepwater Navigation Channel is silted heavily, which brings negative influences on navigation. A two-dimensional numerical model is set up to simulate the hydrodynamics of the Changjiang River Estuary with Delft3D-FLOW in this paper. This model has been validated with the observed tidal level, flow velocity magnitude and direction, and the computed results agree well with the observed data, which also shows the model can well simulate the hydrodynamics of the Changjiang River Estuary caused by the Deepwater Navigation Channel Project. Based on the analysis of computed results, especially the velocity along the South Passage and North Passage, the flood and ebb flow in the Hengsha Passage, and the flow spilt ratio of South Passage and North Passage, it presents that one fundamental reason for the sediment deposition in the upper reach of the Deepwater Navigation Channel is that the velocity along the North Passage is far less than that along South Passage, above all, the velocity in North Passage upstream of the Hengsha Passage is even smaller; another reason is that the flood and ebb flow of Hengsha Passage are large, which weakens the water exchange between the North Passage and South Channel.