Deposition at cross estuary affects the normal navigation of ships and leads to grounding accidents.In order to make full use of the navigation function of the waterway，it is necessary to analyze the causes of navigation obstruction in time and formulate waterway dredging plans to ensure smooth and safe navigation of the waterway.This study takes the cross estuary of Tongyang Canal and Taidong River as the research area，and establishes a two-dimensional Delft 3D water-sediment model to analyze its sediment movement law and geomorphic evolution characteristics in combination with the actual measurement.Based on different dredging elevation and dredging slope，six channel scale schemes are designed，and through simulation analysis，an optimization scheme that takes into account the navigation safety of passing ships and the economic cost of dredging is obtained.This study can provide reference for the channel scale design and optimization of similar crossing estuaries.