As a result of global climate warming, the habitat of endangered waterfowl has been threatened such as the red-crowned cranes. Due to the limitation of the monitoring methods and techniques, the spatial distribution extent of potential habitat in the migration routes of red-crowned crane is unclear, and the impact mechanism of climate change on habitat suitability of red-crowned cranes in migration routes needs to be further studied. On the basis of 138 red-crowned crane samples and 19 environmental variables, an ensemble model was constructed to assess the habitat suitability of the red-crowned cranes in the autumn migration routine of East Asia based on the BIOMOD2 software package. Under the future climate trends of SSP1.2-6, the suitable red-crowned cranes habitats in four different periods (2021--2040, 2041--2060, 2061--2080, 2081--2100) were predicted. The results showed that: (1) The ensemble BIOMOD2 model produced more accurate simulated results compared with the single species distribution model. The most important environmental factors which affected the habitat suitability of red-crowned cranes were elevation above sea level and diurnal temperature range. (2) The simulated area of suitable habitat in the migration route of red-crowned crane is 5.23×10⁵ km² at present. Under the impacts of climate changes, the potential suitable habitat area will reduce to 2.60×10⁵ km², 2.58×10⁵ km², 2.75×10⁵ km², 2.56×10⁵ km² in 2021--2040, 2041--2060, 2081--2080, and 2081--2100, respectively. The area of potential suitable habitats in the migration route will decrease with a range of 8.94% and 14.39% in the future. (3) The predicted suitable habitats in the migration route were mainly distributed in the Zhalong wetland reserve in Heilongjiang Province, the coastal areas along the lower reaches of Liaoning Province, the Bohai Rim, the Yellow River Delta nature reserve in Shandong Province, the Yancheng wetland reserve in Jiangsu Province, the Yellow River and Danjiang wetland reserves in Henan Province, and Shengjin Lake wetland reserve in Anhui Province. The future distribution pattern of suitable habitats is similar to the current distribution pattern of red-crowned crane, and the habitats connectivity between the northeast and the middle of the migration route will decrease significantly. Different kinds of suitable habitats tended to shrink in a large extent, and the decreased habitats was much more than that of the increased habitats. This study is important for the simulation of potential suitable habitats in the migration routes of the endangered waterfowl, and it will be benefit for the conservation and restoration of the endangered waterfowls' habitats under the background of global climate change.