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The evolution of the shoals and vegetation plays an important role in maintaining the stability of the river regime and the estuarine ecosystem. However, the interaction between the evolution of shoals and vegetation dynamic has rarely been reported. In this study, we determined the interaction between the shoal and vegetation evolution of Jiuduansha in the Changjiang River Estuary in the last 30 years. We did this through the collection and summarization of the existing data of the regional hydrological processes, wading engineering, and vegetation, and combined it with the analysis of nautical charts and remote sensing images. During the past 30 years, the expansion of the shoals within the 0 m isobath in Jiuduansha was obvious, with an increase of 176.5%, while the expansion of the shoals within the 5 m isobath was relatively slow. The regional hydrological characteristics in the Jiuduansha area changed dramatically, especially the sediment discharges. The area of vegetation in Jiuduansha increased from 9.1 km2 in 1990 to 65.68 km2 in 2015, while the variations in the different vegetation types were different. The best combination of environmental factors with a significant correlation on the shoals within the 0 m isobath is the area of Spartina alterniflora and Phragmites australis. The evolution of Jiuduansha shoals was significantly affected by the variations in hydrological characteristics. Meanwhile, on a long-term scale, the expansion of the shoals could promote the regional vegetation expansions due to the suitable elevation and environmental conditions it provides. The interaction between the shoal and vegetation evolution varied in the different vegetation types and different elevations. In the future, long-term monitoring and detailed data are needed to the systematical analysis of the interaction between the hydrological processes and the evolution of the shoal and vegetation.