Coastal wetlands form a transition zone between terrestrial and marine environments and provide important ecosystem services. Land-use change in the coastal zone has a substantial effect on habitat connectivity and biodiversity. However, few studies have characterized the effects of land-use change on coastal habitat connectivity. We conducted remote sensing analysis, modeling with the Integrated Valuation of Ecosystem Services and Trade-offs model, geospatial analysis, and habitat connectivity analysis to evaluate historical spatiotemporal changes in the habitat quality and habitat connectivity of migratory shorebirds in the Yellow River Delta, which is an important stopover site along the East Asian–Australasian Flyway migratory route. Several high- and medium-quality areas have been converted to industrial mining and mariculture sites because of land reclamation. The probability of connectivity decreased by −66.7% between 1975 and 2020. Approximately 71.0%, 11.6%, and 5.8% of patches with high importance have been converted to non-habitat patches, habitat patches with medium importance, and habitat patches with low importance, respectively; approximately 58.9% and 11.7% of the patches with medium importance have been converted to non-habitat patches and habitat patches with low importance, respectively. The total priority conservation area was 389.4 km2, and 125.0 km2 (32.1%) of this area remains unprotected; these unprotected areas are mainly distributed in the northwestern and eastern parts of the Yellow River Delta. We recommend that the boundary of the Yellow River Delta National Nature Reserve be expanded to incorporate these unprotected areas.