In order to study the adjustment characteristics and response of the important shoals in the bar area of the Yangtze River estuary under the influence of sediment discharge decreasing and human activities, this article took the Hengsha shoal, the Jiuduansha shoal and the eastern Nanhui beach as examples. The measured hydrological and topographic data were used to investigate the morphological adjustment of the shoals and the response to changed environment. The results show that in recent years, the two-dimensional geomorphology of the shoals were shrank in the bar area of the Yangtze River estuary, and the tail of the shoals stop progradation in general. The Hengsha shoal and Jiuduansha shoal had different degrees of tidal creeks development; Empirical relationships were developed between the areas of the Hengsha shoal and the previous seven-year average fluvial erosion intensity during flood seasons. This relationship can be used to reflect the change tendency of shoal’s area with the altered flow and sediment regime; The estuarine regulation project can restrain some part of the shoal’s erosion, which was caused by the variation of the flow and sediment conditions. However, the estuarine regulation project may have a slow and long-term cumulative impact on the surrounding regions.