Abstract: Affected by the high tide and big waves caused by the super typhoons "Hato" and "Mangosteen", both sides of the Maliuzhou Waterway in Modaomen of the Pearl River Estuary were seriously damaged, so higher requirements were put forward for the improvement of the flood prevention (tidal) system. In this study, the Maliuzhou Waterway was taken as the research area, by constructing a two-dimensional tidal flow mathematical model for the entire Pearl River Estuary and the local Maliuzhou Waterway, four groups of typical hydrological conditions including flood "2005.6", moderate flood " 2002.6", low water "2001.2" and "9316" storm surge (the total period is 88 hours from 0:00 on September 16 to 20:00 on September 19, 1993) were selected to reinforce the two banks. The river situation in the water area after the lifting is analyzed. After the embankment is reinforced and lifted, the hydrodynamic flow path is clear and the flow pattern is smooth. The mathematical model constructed in this study has good adaptability to the hydrodynamic simulation of Modaomen in the Pearl River Estuary, and the improvement plan of the flood prevention and tide system has guiding significance for the estuary area.