The hydrological situations of wetlands are critical to the habitat qualities of wintering migratory birds. It is of great value to evaluate the habitat vulnerabilities within more precise intervals of water levels and quantitatively assess the influences of water level changes. The findings are advantageous for managing wetland ecosystems and for migratory bird habitat protection. This study identified the ideal habitats for wintering Siberian cranes in Poyang Lake wetland within 1-meter water level intervals (from 5 to 16 m) based on the Landsat thematic mapper (TM), enhanced thematic mapper plus (ETM+), and operational land imager (OLI) remote sensing images taken on multiple dates in the past 30 years. Three indicators—sustainability, stability, and variety—were used to evaluate the vulnerabilities of crane habitats within various water level intervals; the spatial variations and distribution patterns of the habitat vulnerabilities were further explored. The explanatory powers of water level intervals (and others) and their paired interactive effects on the habitat vulnerabilities were quantified using the geographical detector method. The results showed that crane habitat vulnerabilities were significantly sensitive to the water level changes of Poyang Lake; the habitat vulnerabilities and their spatial distribution patterns both exhibited specific tendencies with water level increases. A water level of 12 m was identified as the potential upper threshold for the maintenance of sustainable crane habitats and a water level interval of 9–10 m was expected to be the optimal interval for facilitating the aggregation features of crane habitats. The water level interval was identified as the most dominant factor in habitat vulnerability. It explained 14.46%, 42.89%, and 21.78% of the sustainability, stability, and variety of crane habitats; the numbers were expected to increase to 22%, 49.25%, and 25.84%, respectively, with water level intervals interacting with other factors. This article provides a novel perspective in evaluating the habitat vulnerabilities of wintering migratory birds and quantifying the responses to water level changes in wetlands; the proposed approaches are applicable and practicable for habitat vulnerability assessments of other wintering birds in other typical wetlands.