A 3D tidal current and sediment mathematical model under the effect of wind and wave is set up and used to simulate the current field and sediment concentration field under typhoon“WIPHA”around Lianyungang sea area. The computed results and the field measured data are compared and verified. The verification shows that the simulated result tallies well with the field observation data. On this basis, the mathematical model is used to simulate the sediment deposition of 300 000 DWT deep-water channel of Lianyungang port during“WIPHA”typhoon. The deposition thickness of the channel is presented, which can provide a basis for the design of the navigation channel.