The alpine musk deer (Moschus sifanicus) is an endangered ungulate for which captive breeding is being promoted as the best way to conserve the species. Studies of animal personality could be an important path to facilitate captive breeding practices, yet only a few studies have been carried out in this field for musk deer. Focal sampling and scan sampling were used to quantify personality traits (measured by activity, territoriality, stereotypy, exploration, and behavioral redundancy) of alpine musk deer at the Breeding Center for Alpine Musk Deer, Xinglongshan National Nature Reserve, Gansu Province, and to investigate the effects of the captive musk deer's personality traits on musk secretion. We also assessed the relationships between personality traits and both gender and age during both mating and non-mating seasons. We found that older individuals were less active during both mating and non-mating seasons, and were less territorial during non-mating season (all P < 0.05). Females were more active than males (P < 0.05). Alpine musk deer were more active and territorial during mating season than during non-mating season, and activity and territoriality were positively correlated in both seasons (P < 0.05). Males with higher activity and territoriality had more musk secretion (P < 0.05). Our results showed that personality traits of musk deer varied between age and gender, but there was consistency across mating and non-mating seasons. Personality traits, especially activity and territoriality, can predict the musk secretion by males. Quantitative analysis of musk deer personality is an appropriate approach for the development of musk resources.