The Yangtze River Estuary is a complex ecosystem based on the interaction of salt and fresh water. It is an important node on the East Asian-Australasian Flyway for migratory birds and an indispensable "three sites and one corridor" for the life cycle of rare aquatic animals such as Chinese sturgeon. However, due to its location in a highly urbanized area, the region is significantly affected by human interference, resulting in prominent issues such as a decline in biodiversity and ecological service functions. There is an urgent need for systematic analysis and assessment of the ecosystem characteristics and conservation value of this region, as well as the identification of critical ecosystem areas, to achieve spatial integration of conservation and development. This study systematically identified and analyzed the ecosystem characteristics of the Yangtze River Estuary, and constructed a comprehensive evaluation system for conservation value from three levels: national representativeness, ecological importance, and conservation foundation. It systematically analyzed and evaluated the conservation value of the Yangtze River Estuary, and identified critical conservation areas. The results showed that the ecosystem of the Yangtze River Estuary exhibited the characteristics of 'three highs and one low', indicating extremely high conservation value. Coastal wetland ecosystems, birds, and aquatic biodiversity conservation all demonstrated significant national representativeness, coupled with high sensitivity, high risk, and high ecological service function characteristics. The conservation value of the Yangtze River Estuary exhibited spatial heterogeneity. It was high in the eastern region and water source protection areas, but relatively low in the third-level branching channels. Critical protected areas were concentrated around Chongming Dongtan, Beihu, Jiuduansha, the western part of Hengsha, as well as reservoir areas. We suggest that relevant departments further advance the planning and construction of a national park in the Yangtze River Estuary, integrate various types of nature reserves, achieve ecological integrity protection in the Estuary, and promote the national strategies of comprehensive protection of the Yangtze River and integration of the Yangtze River Delta region.