Based on the Environmental Fluid Dynamics Code (EFDC), a three-dimensional baroclinic model for lower reaches of the Yangtze River, Yangtze River Estuary, Hangzhou Bay and the adjacent sea areas was established with the sigma-coordinate in the vertical direction and the orthogonal curvilinear coordinates in the horizontal direction. The fine silt particle tracers were injected during different tides with the calibrated three-dimensional numerical model in the Yangtze River Estuary to simulate the migration tracks of the tracers in the following three days, and thereby study the migration behavior of the fine silt particles of dredged sediment after dumping at different locations in the navigation channel in the Yangtze River Estuary. The study shows that the particle paths of the tracer particles basically migrate to the open sea along the middle axis of river course in the form of reciprocating oscillation, the migration and diffusion directions of tracer particles are basically parallel to the navigation channel in guide levee, similar to long belt distribution, and the tracer particles migrate to the sotheast out of the guide levee. The particle which is on the southern and northern sides enter groin and cross the navigation channel in the process of movement, and is easy to deposit in the navigation channel. The migration tracks of the particles released at different layers are basically similar at the same release station, but specifically different, varying at different cross sections. The result can be used for the choice and evaluation of dredging schemes in the Yangtze River Deepwater Navigation Channel.