The water depth of navigational channel in the south channel and north passage is over 12.5 m after the Yangtze estuary deepwater channel regulation project. The river regime and flow dynamics condition of the Yangtze estuary changed after the project. The characteristics of bed transformation in the Yangtze river estuary is studied with actual underwater geomorphic data. The 2-D numerical simulation of tidal current SWEM2D of Estuarine & Coastal Science Research Center of Shanghai is used to simulate the flow field in the Yangtze estuary. The change of flow ration of south channel and north channel, south passage and north passage, which is the main factor to the Yangtze estuary, is analyzed. The main reasons for the change of flow ration are also given.