The Fenghe River Estuary (FRE), a long-narrow estuary located in the West Coast New Area of Qingdao, China, has suffered severe sediment siltation in the downstream of a tidal barrier over the past decades. In order to relieve the sediment siltation and promote local economic development, a restoration scheme with new shoreline and bathymetry was proposed for the FRE. In this study, a wave-current-sediment coupled model was established for the FRE based on the numerical model MIKE21, which was well validated against the observation. The model was then applied to estimate hydrodynamic and morphological responses of the long-narrow estuary to the restoration scheme and a major storm. The numerical results indicate that the restoration scheme has a great influence on the current fields in the estuarine channel, resulting in the current speed in the channel to be more spatially uniform. Under the restoration scheme, the spatial pattern of suspended sediment concentration in the estuary is redistributed due to the change of local tidal asymmetry associated with geometry and topography variation. The interaction between wave and current during a storm increases bed shear stress on the tidal flat, leading to large erosion on the tidal flat and severe sediment siltation in the estuarine channel.