Recent research on short-term topographic change in the Yangtze Estuary channel under storm surge conditions is briefly summarized. The mild-slope, Boussinesq and action balance equations are compared and analyzed. The action balance equation, SWAN, was used as a wave numerical model to forecast strong storm waves in the Yangtze Estuary. The spherical coordinate system and source terms used in the equation are described in this paper. The significant wave height and the wave orbital motion velocity near the bottom of the channel during 20 m/s winds in the EES direction were simulated, and the model was calibrated with observation data of winds and waves generated by Tropical Cyclone 9912. The distribution of critical velocity for incipient motion along the bottom was computed according to the threshold velocity formula for bottom sediment. The mechanism of rapid deposition is analyzed based on the difference between the root-mean-square value of the near-bottom wave orbital motion velocity and the bottom critical tractive velocity. The results show that a large amount of bottom sediments from Hengsha Shoal and Jiuduan Shoal are lifted into the water body when 20 m/s wind is blowing in the EES direction. Some of the sediments may enter the channel with the cross-channel current, causing serious rapid deposition. Finally, the tendency of the storm to induce rapid deposition in the Yangtze Estuary channel zone is analyzed.