The storm impact on coastal environment is complex and systematic. With a validated numerical model, this study quantitatively investigates the effects of a historical storm process on the morphodynamic evolution of an unsheltered Nanpu channel-shoal system (NS) in the Bohai Sea, China. Results show that the storm event in October 2003 induced a destructive erosion in the tidal flats during the entire storm period. The channel also suffered erosion, however, it rapidly restored after this storm. Numerical estimations also confirm that wave and wind-driven current dominate the erosion of tidal flat and channel, respectively. Wind-driven current can further enhance the erosion on the tidal flat by intensifying the wave-current interaction, while surge plays a minor role in the channel-shoal evolution. The morphological evolution pattern of NS varies as a function of wind direction and wind speed, where three morphological evolution patterns appear as the wind speed growth in the investigated NE and NW wind directions. In the study area, NE strong wind usually produces flooding disasters and erosion of NS, while NW strong wind can induce severe tidal flat loss and channel accretion. Although this study is based on a site-specific model, the findings will provide valuable insights into the morphological feedbacks under destructive storm and hence assist in making efficient coastal management strategies in unsheltered coasts.