Tongzhou shoal and Baimao shoal are two major obstacle shoals of the 12.5 m deep water channel extending up to Nanjing in the Yangtze River. The engineering river reach is influenced by both river discharge and tide, hydrodynamics is complicated and river bed is active in siltation and erosion. Two-dimensional numerical tidal model is set up to study nonuniform nonequilibrium sediment movement in the three sand shoals (Fujiang shoal, Tongzhou shoal, Baimao shoal). Based on the study on the sediment carrying capacity formula and suspended and bed sediment exchange mode, the paper calibrates and verifies the model by measured hydrology and field bathymetry data. The model is applied to the 12.5m deep water channel phase I project to analyze the influence of regulation works and affords technical support for the engineering design.