The alpine musk deer (Moschus chrysogaster) is a key species of some terrestrial ecosystems, it has an important economic and conservative significance as a kind of medical animal in China. Due to the interaction between natural forces and human disturbance, the habitats of alpine musk deer are fragmented and isolated in different mountains and the populations are confronted with many problems of survival. In this paper, we discuss the impact of habitat fragmentation and isolation on alpine musk deer populations based on the investigation on the population densities and sizes and environmental factors in different reserves, as well as on the analysis of its ecological adaptability. We found that the alpine musk deer has strong ecological adaptability; the population development of alpine musk deer may benefit from the reduction of the forest area and even from the fragmentation and isolation of the habitat to a certain extent. However, deforestion should not be encouraged only for the alpine musk deer population, but should also be based on the overall consideration of biodiversity conservation.