The third pPhase of Guangzhou seaward channel project and auxiliary projects is a momentous project, so it is necessary to study the effects on the sediment transport and evolution of flats and channels of the Inner Lingdingyang before the implementation of the project. Base on the calculation and analysis by introducing 2D numerical model of tidal current and sediment, it reveals that the effects will primarily occur in the Jiaomen extending riverway, the west shoal and channel of the Inner Lingdingyang, and less effect will occur in the upper section of the extending riverway of Jiaomen and the water areas to the east of Fuzhou riverway and Longxue island. From the long-term view, the evolution in Fuzhou riverway, Jiaomen extending riverway, and the inner Lingdingyang will not be serious, scouring and silting speed will slow down gradually, and the structure of three shoals and two channels will keep unchanged.