The Whooper Swan is a representative species among large and medium-sized migratory waterbirds. Predicting suitable winter habitats and identifying protection gaps for the Whooper Swan can provide a significant basis for protecting other endangered species and their habitats. Based on the Whooper Swan winter distribution data from 2003 to 2023 and incorporating factors such as climate, anthropogenic disturbances, and land-use type, we utilized the Maximum Entropy (MaxEnt) model to predict the suitable winter habitat of the Whooper Swan and evaluated the effectiveness of the Xinjiang protected area system in protecting Whooper Swans in Xinjiang. The results showed that the total suitable winter habitat for the Whooper Swan is 65,359 km2, mainly distributed in Bortala in southern Xinjiang and Tacheng, Altay, and Ili in northern Xinjiang. The key factors affecting the suitability of the Whooper Swan's winter habitat are land-use type, distance to water surface, bio7 (annual temperature range), distance to cultivated land, bio3 (isothermality), and distance to rivers. Currently, the protected area system, mainly composed of nature reserves and wetland parks, covers 10304 km2 (15.77%) of suitable wintering habitat for the whooper swan. There is a considerable gap in suitable winter habitats, which is primarily concentrated in densely populated areas that cannot be covered by protected areas. Based on the above results, we suggest strengthening the strict protection and management of the Whooper Swans within the existing protection system and exploring effective protection measures by minimizing human interference and supplementing food for swans outside the protection system. This will ensure that these endangered birds can successfully overwinter in Xinjiang.