The Helan Mountains, situated in the heart of the desert, act as a dividing line between China’s arid and semi-arid zones. Often referred to as a ”desert oasis,” they create an ecological island with a uniquely distinctive geographical location, making this area a focal point of contemporary research. Ungulates play a critical role in this ecosystem. The Alashan wapiti (Cervus canadensis alashanicus), an isolated population of China’s smallest wapiti (Cervus canadensis) subspecies, is found exclusively within the Helan Mountains Nature Reserve. The conservation of this isolated population is fraught with challenges, particularly during winter, the harshest season for northern ungulates. Winter habitats are crucial for ensuring population stability. Therefore, we used certain methods, such as factor screening and model parameter optimization to assess habitat suitability using multi-scale species distribution models. The optimized results show that suitable habitats overlap with areas of high vegetation coverage in the Helan Mountains, covering just 588.32 km², which is less than a quarter of the reserve’s total area. The bare land area and winter NDVI are the two primary factors influencing habitat suitability, with other factors having minimal impact, underscoring the critical importance of food resources for the Alashan wapiti. The limited availability of these resources poses significant conservation challenges. Our findings provide a more precise foundation for targeted habitat protection and restoration efforts. We recommend enhancing the protection and restoration of food resources, effectively conserving vegetated areas, and preventing desertification.