Protected areas are essential for the conservation of biodiversity. However, the rapid expansion of urbanization and the intensification of human activities have significantly disrupted environmental integrity, leading to a continuous deterioration in both the quantity and quality of large ecological patches. This has further diminished the connectivity among ecological patches, leading to significant consequences for regional biodiversity conservation. Taking Poyang Lake as a case study, which serves as a crucial wintering habitat for migratory birds along the East Asia–Australasia flyway, this research employs ArcMap technology. It considers various factors including land use type, slope, and elevation to evaluate habitat quality and degradation through the application of the InVEST model. Additionally, the study utilizes the minimum cumulative resistance (MCR) model alongside circuit theory to delineate ecological corridors within the area and to establish a comprehensive ecological network system. The research results in this paper are as follows. (i) During the period from 2000 to 2020, there was an overall decline in habitat quality within the study area, indicating a clear trend of habitat degradation. However, it is worth noting that there was an increase in habitat quality in certain local areas within the protected area. (ii) The ecological resistance values in the core area of the migratory bird reserve in Poyang Lake are generally low. However, the ecological resistance values of the habitats have shown a consistent increase from 2000 to 2020. Additionally, there has been a significant decrease in the density of ecological corridors during this time period. (iii) Over the period from 2000 to 2020, both the number and connectivity of ecological corridors decreased and their integrity and functionality degraded. Consequently, this weakened role of the ecological network has had implications for maintaining regional biodiversity and ecosystem service functions. The findings indicate two conclusions. (i) Ecological connectivity is essential for the conservation of migratory bird habitats. Strengthening control measures aimed at expanding ecological corridors can effectively safeguard flagship and umbrella species, thereby promoting biodiversity conservation. (ii) The establishment of ecological corridors can help reconcile conflicts between conservation efforts and development objectives. This reconciliation carries significant theoretical implications for fostering a harmonious coexistence between humans and birds in Poyang Lake’s migratory bird sanctuary.