The proposed excavated-in harbor and shipping channel are located in the adjacent region of Hengsha Shoal in the outer Changjiang River mouth. Accumulation of huge amount of sediment from the upstream Changjiang River occurs in the river mouth, resulted in the large delta area on both land and submarine. Hengsha Shoal is recognized as one of the three largest shallow shoals, with Chongming East Shoal and Jiuduansha Shoal in the sandbar region of Changjiang River mouth. It shows stable location and bathymetry pattern in the long-term history, which indicates it's an excellent location for a new harbor. During its long history of the submarine delta, the bathymetry is mainly flat and under the deposition effect of delta. With the recent deceasing of the sediment load from the Changjiang River, there is small evolution of the bathymetry. This is favorable for construction of the shipping channel into excavated-in harbor. This paper mainly focuses on the morphological stability of the bathymetry and its evolution trend, to provide some basic support for the new deep harbor.