With the intensification of human activities and the frequent occurrence of extreme climate events, the Yangtze Estuary has faced a series of challenges, including a sharp reduction in sediment supply, abnormal drought during flood seasons, and frequent extreme flood and tidal disasters. These issues have led to significant adjustments in the estuarine geomorphology. Based on hydrological, sediment, and topographic data from 1958 to 2022, this study investigates the evolution characteristics and patterns of the North and South Branches of the Yangtze Estuary. The driving factors and recent differential evolution characteristics of the North Branch and the South Branch are analyzed. Management strategies tailored to the evolution characteristics of the North and South Branches are proposed. The research results indicate the North Branch entrance section has exhibited a pronounced sedimentation trend recently due to factors such as reclamation projects and natural siltation. In contrast, the South Branch reach demonstrates a channel-scouring tendency under the combined effects of sharp reductions in upstream sediment supply, enhanced runoff dynamics, and the implementation of regulation projects, while maintaining generally stable overall channel regime. This study provides scientific and technical support for the comprehensive management of the Yangtze Estuary.