Habitat assessment and prediction is the base for protection of endangered species. In this paper, MAXENT and ENFA were applied to predict habitat for forest musk deer in Qinling mountain range, with evidence data of this species, and other environment factors. Prediction results were evaluated by both of threshold-dependent and threshold-independent methods. And the environmental factors and habitat selection of forest musk deer were then analyzed. Results showed that both models showed good prediction ability, and MAXENT gave a better prediction than that of ENFA. The habitat of forest musk deer was mainly distributed in Taibai Mountain and surrounding areas in Qinling mountain range, with the total area of 10764.4km². The current nature reserves protected only 3500.9km² of the habitat of this species, and 67.5% of the habitat was in conservation gap. For effective protection of forest musk deer in this area, it is necessary to adjust the current nature reserves for covering most of the concentration habitat, and to restore the corridors among habitat patches.