Abstract: In November 2015, the port area of Binzhou Harbor in Shandong Province experienced a sudden siltation process due to strong winds, leading to severe siltation in the existing 30,000-ton navigation channel. The construction and development of Binzhou Harbor, and the swift siltation management of navigation channels are critical. Based on the three-dimensional tidal current and sediment model FVCOM and the wave model SWAN, considering the interaction between hydrodynamics and sediment, a new three-dimensional hydro-sediment model based on novel three-dimensional radiation stress was established. This model was validated through the simulation and analysis of tidal current fields, wave fields, and suspended sediment fields based on full-tide hydrological observation data from 2014. Furthermore, the siltation volume under strong wind conditions for the current navigation channel, and for extensions of the outfall dyke head to 7.5 m and 9.0 m scenarios were calculated, analyzing the reasons behind channel siltation. Comparative results of the simulations demonstrate that the further the extension of the outfall dyke, the greater the reduction in channel siltation, but the per-width reduction in siltation will gradually decrease with continued extension. This study provides a reference for navigation channel siltation control and siltation reduction measures.