The planed excavated-in harbor in the Hengsha Shoal, located in the river mouth of Changjiang Estuary, has large spatial coverage, which certainly would have significant influence on the hydrodynamics around the local and adjacent regions. This paper focuses on the hydrodynamic influences of the new harbor based on a validated high-resolution unstructured-grid FVCOM model. The modeling results of current field and characteristics at some typical locations show that neither the South nor the North Plans would create significant influence on the hydrodynamics in the North Channel and North Passage, while the South Plan shows more obvious impact on the outer shipping channel of the Deep Waterway Project. Both plans indicate the currents in the North Channel show increasing dominant of alternating current, while the South Plan would produce more significant cross-channel current at the outer region of excavated-in harbor.