To improve habitat conservation and management of the Khulan (Equus hemiomus hemionus), we assessed the habitat suitability of this species in the Kalamaili Mountain Nature Reserve. Distance from water point, slope, vegetation type and human activities were selected as factors for habitat suitability assessment, and the habitat evaluation model for the assessment was conducted with GIS. In the absence of human activities, the total area of potential suitable habitat was 9,784 km2, 8,090 km2, 9,379 km2 and 10,856 km2 during the four seasons, accounting for 54.4%, 44.9%, 52.1% and 60.3% of the total reserve area, respectively. However, the reserve was negatively affected by a national highway, mine exploration, and grazing livestock. As a result, a large amount of suitable habitats were lost in the reserve. Especially in winter, nearly 6,629 km2 of suitable habitats were lost in the reserve, which accounts for 61.1% of suitable habitat during these months. Based on these results, the following measures were put forward to protect the population of Khulan: (1) strengthen protection of water resources; (2) limit the population size of livestock in the reserve during winter months; (3) regulate and/or restrict human activities in the reserve; and (4) remove border fences and rebuild the population migration and connection routes for the Khulan between China and Mongolia.