This study investigates the impact of coastal tidal flat reclamation on the protection of rare bird habitats, with a particular focus on the red-crowned crane, a species of significant conservation concern. In the context of China’s rapid economic growth, large-scale reclamation of coastal wetlands has led to severe damage to vital bird habitats. These areas, once critical for migratory and breeding birds, are increasingly being transformed into urban or agricultural land, leading to a decline in biodiversity. By analyzing the case of the Yancheng Wetland National Nature Reserve for Rare Birds, the paper integrates water quality models with Geographic Information System (GIS) technology to assess the effects of reclamation intensity on environmental carrying capacity. This approach enables the identification of a critical threshold at which reclamation becomes unsustainable for the local ecosystem. The study offers valuable insights into how coastal tidal flats can be utilized sustainably, emphasizing the need to balance ecological protection with resource development. It proposes that maintaining the reclamation intensity below a certain limit is crucial for preserving the delicate balance between environmental health and economic growth.