Based on a series of bathymetric data from 1998 to 2016, the new trends of river channel evolution of the Yangtze River estuary under the influences of inflow and sediment variations and human activities are studied. The results show that in the past 20 years, the channel morphology of the Yangtze River estuary has been generally stable, but the downstream channel of the south branch has changed from net siltation to net scour, the channel of the estuary has been scoured and the volume has been expanded, and the length of the channel bar shoal outside the estuary has been shortened. The stability of channel morphology is promoted by the estuary beach enclosure, artificial protection of sandbank in the middle of the river and the flood control and peak elimination of the Three Gorges project. The decrease of sediment and estuary beach enclosure promote the transformation from net siltation to net scour in the downstream channel of the south branch. 2002 and 2003 were basically the time node of the transformation, which corresponds to about 254 million tons of annual sediment transport. In the future, the fluvial sediment is likely to remain at a low level below the critical value for a long time, and the Yangtze River estuary will maintain a slow erosion trend under the stable channel morphology.