Population survey of wild musk deer (Moschus chrysogaster) in Xinglongshan National Nature Reserve (XNNR) of Gansu Province was conducted by the line-transect surveying, pellet-group surveying and repeated surveying. The population distribution, size, density and influencing factors were determined. The results showed that there were 1159±275 wild musk deer in the XNNR and the average population density was (3.51±0.83)km². The population size and density of wild musk deer were different in various habitats of XNNR. Nearly 70% (807±170) wild musk deer were in the shrubs with a population density of (6.49±1.63)km². The coniferous forest had the highest population density, i.e. (8.85±83.25)km², with 123±45 musk deer, while the mixed coniferous and broad-leaved forest was the least distributed, only 41±15 deer with a population density of (5.00±1.84)km². No wild musk deer distributed in artificial forest habitat. In XNNR, the different distribution of wild musk deer among habitats is related to the habitat suitability. Ecological needs to the food, heat preservation and sheltering are the key factors that restrict the distribution and population size of wild musk deer. Moreover, the population distribution differences of wild musk deer in XNNR is related to the intensity of artificial stresses including regional economic development and marginal agricultural activities. It is suggested that measures such as human disturbance reduction, surface vegetation management, artificial forest management, and eco-tourism improving should be taken in XNNR to improve the habitat suitability and promote the rapid recovery and growth of wild musk deer population.