In sexually dimorphic species, males and females may select different habitat for greater fitness. However, the key factors that play a leading role between sexes in habitat selection are still poorly understood. In this paper, we investigated the possible causes of the differences in habitat preference between male and female Siberian ibex (Capra sibirica) living in the Tianshan Mountains (China). Using the Maximum entropy model, we found that the ruggedness and elevation of the terrain were the most important factors affecting habitat selection in Siberian ibex. Females preferred the most rugged terrain to increase the security of their young and themselves, while males favored moderately rugged terrain to provide sufficient safety from predators, and availability of suitable forage simultaneously. Females used a wider variety of elevations to search for newly emerged vegetation for its higher nutritional value, while males preferred more elevated slopes to avoid the higher temperatures and greater presence of biting insects found at the lower elevations. In addition, females were associated more with rivers due to their higher water demands. The differences in habitat selection between Siberian ibex males and females depend on multiple considerations, but only a limited number of key factors determine their actual distribution.