The wetlands where the migratory waterfowl stop during their migration, also called stopover wetlands, are important nodes where migratory waterfowl supplement their energy and food. The Siberian crane (Grus leucogeranus), a wetland obligate endangered species, is highly dependent on a series of stopovers on the migration route. Although some conservation measures have been adopted in China, it is still necessary to develop an appropriate management strategy to preserve this endangered species at different stopover areas. This paper used maximum entropy modeling to evaluate habitat suitability for the migration of the Siberian crane. We found that vegetation community type and water depth are the most important factors affecting the distribution of the Siberian crane during the migration period. For Siberian crane migration, the most suitable water depth does not exceed 60 cm, the desirable land cover type is swamp, the most suitable community is Phragmites-Sparganium, the most suitable vegetation coverage is from 8% to 35%, the distance from a residential area is over 2800 m, and the distance from a road is over 2000 m. On this basis, some specific conservation strategies are proposed for better protection and management of the Siberian crane’s habitat. These results can serve as a reference point for the preservation and management of the potential habitats of similar endangered waterfowl.