The survey of habitation and distribution for Equus kiang and Bos grunniens was carried out using the transects and quadrat sampling methods in the east part of Altun Mountain Nature Reserve, Xinjiang during 2012 and 2013. Three transects amounted to 146.9 km and 128 quadrats were set for further analysis. The distribution of two species indicated that Equus kiang mainly appeared in Yixiekepati desert grassland while Bos grunniens preferred to Abadiba meadow grassland.The selection of environmental variables and the influential factors in habitat selection by the two species were analyzed by Vanderloeg and Scavia index as well as factor analysis. The difference of habitat selection was analyzed by using Independent-Sample Test. The results showed that E. kiang prefer the habitats of alpine deserts with the following features, vegetation coverage of <70%, slope of 2°-5°, altitude of 3 800-4 000 m, and soil pH of 8.0-8.5. B. grunniens prefer the alpine desert steppe or swamp meadow with the following attributes: vegetation coverage of >70%), slope of 5°-15°, altitude of 4 200-4 600 m, soil pH of 7.0-8.0. Habitat selection by E. kiang was mainly influenced by vegetation type and slope while habitat selection of B. grunniens was influenced by vegetation coverage. Although there were partial overlaps in resource utilization between two species, significant difference in selection of vegetation coverage and height, altitude and slope were observed for these two species (P<0.05).