A depth-averaged 2D numerical model is set up to simulate the hydrodynamics of the Deepwater Navigation Channel of the Yangtze estuary due to the regulation engineering with MIKE21, which has been well calibrated and validated with the observed data of the tidal level, flow velocity and flow direction in the Yangtze estuary. The simulated results indicate that after the regulation engineering of the Deepwater Navigation Channel,1): The increase of tide amplitude at the lower reach, middle reach and fish mouth project part of the channel are about 0–0.2 m, 0.3–0.5 m and 0.2–0.3 m, respectively;2): The embankment and the spur dike are submerged during the flood tide. While at ebb tide, the embankment and the spur dike are exposed due to the decreasing of the tidal level.