Suspended sediment plays a major role in estuary morphological change and shoal erosion and deposition. The impact of storm waves on sediment transport and resuspension in the Yangtze River Estuary (YRE) was investigated using a 3D coupling hydrodynamic-wave model with a sediment transport model during Typhoon Ampil. This model has been validated in field observations of water level, current, wave, and sediment concentration. The model was run for tide only, tide + wind, tide + wind and wave forcing conditions. It was found that: (1) typhoons can increase the suspended sediment concentration (SSC) by enhancing bed shear stress (BSS), especially in the offshore area of the YRE, and there is hysteresis between SSC and BSS variation; (2) exponential and vertical-line types are the main vertical profile of the SSC in the YRE and typhoons can strengthen vertical mixing and reconstruct the vertical distribution; and (3) waves are the dominating forcing factor for the SSC in the majority of the YRE through wave-induced BSS which releases sediment from the seabed. This study comprehensively investigates the spatio-temporal variation in SSC induced by Typhoon Ampil in the main branch of the YRE, which provides insights into sediment transport and resuspension during severe storms for estuaries around the world.