Poyang lake area (1000–3246 km²) is the most important wintering ground for the globally critically endangered Siberian crane (Leucogeranus leucogeranus). More than 98% of the Siberian crane population overwinters in Poyang lake area. Remote-sensing and the spatial analysis tools of geographic information system (GIS) technology were used to assess the suitability of the habitat for wintering Siberian cranes in Poyang lake area at different water levels. The results demonstrated that as the water level increased within the range of 7.93–12.16 m, the area of unsuitable habitat increased gradually, but the areas of good, fair and poor habitat decreased. When the water level reached 12.16 m, good habitat for Siberian cranes covered an area of only 3005 ha, which is only 0.93% of the area of the total lake area. When human disturbance factors including vehicles, fishing and construction activities were added to the analysis of the current distribution of Siberian crane habitat, the results again indicated that the area of good habitat decreased with an increase in water level within the range of 7.93–12.16 m. Additionally, the areas of good habitat occurred primarily in the region of two national nature reserves, which are the Poyang Lake National Nature Reserve and the Nanjishan National Nature Reserve. Our study provides important data and an important theoretical basis for water level management and nature reserve construction in Poyang lake area.