This species is found on barren plateaus at high altitudes, where it occupies meadows, fell-fields, shrublands or fir forests, typically preferring shaded steeper slopes with less human disturbance. In western Sichuan, where it overlaps the distribution of M. berezovskii, the alpine musk deer inhabits the higher elevations (above 2,000 m asl, usually 4,000-4,500 m asl), compared with the 1,0002,500 m altitudinal range of M. berezovskii.

It is predominantly a browser, feeding mainly on shrubs, forbs, leaves, moss, lichens, shoots, grasses, and twigs (Green 1987). The proportion of leaves and tender shoots in the diet is highest in spring and summer, buds and flowers in late summer, and leaves, twigs and flowers of forbs and shrubs later in the year (Wilson and Mittermeier 2011, Syed and Ilyas 2012).

Its main predators include yellow-throated marten, fox, wolf, and lynx. Snow leopard reportedly preys on the species in Nepal (Aryal et al. 2010) It is generally solitary and crepuscular (Harris and Cai 1993). Population density varies from 3.9 /km² in more arid habitats to 71 /km² in areas with higher rainfall. Densities are lower in areas with heavy snow cover and where there are more competitors (goral, serow and domestic cattle).

Breeding occurs primarily in November-December, with the resulting offspring being born from May to June. After birth, young deer lie hidden in secluded areas, essentially independent of their mothers except at feeding times. This hiding period may last up to 2 months. Gestation is variously reported at from 150-195 days (Hayssen et al. 1993) and give birth to one offspring (twins are sometimes reported by documentation is lacking). Fawns wean at 3-4 months, are sexually mature at 16-24 months.

Alpine musk deer is sedentary, tending to remain within defined home ranges. In females these are about 125 acres in size, while males will control a territory that encompasses the ranges of several females, possibly defending it against other males. The species is not known to migrate. Communication between individuals is thought to be based primarily on their sense of smell, due to the high development of the glands of musk deer. It is primarily silent, musk deer will emit a loud double hiss if alarmed.

This species occurs from the highlands of central China (the Helan mountains form the northern edge of the distribution), south and west to the Himalayas, extending to eastern Nepal, Bhutan, and northeastern India (Sathyakumar 2002, Wemmer 1998). It is widely but discontinuously distributed across the mountainous parts of the Himalayas (Aryal et al. 2010). Records from Afghanistan and Pakistan refer to Moschus cupreus. This species is found at elevations of 2,000-5,000 m asl.

Within China, which comprises the bulk of its range, it is found in southern Gansu, southern Ningxia, Qinghai, western Sichuan, southern Tibet, and northern Yunnan.

This species is listed on CITES Appendix II in China, and on Appendix I in the other countries within its range. The sifanicus subspecies is on the China Red List as Critically Endangered (A1acd+B1ab(i,ii,iii)), and was changed from category II to category I on the China Key List in February 2003. Captive breeding, primarily for commercial musk production, occurs in various places in China, and might have some conservation benefit. However, to date, there is little evidence that the availability of musk from captive-bred animals has had a positive conservation impact (Parry-Jones and Wu 2001, Green et al. 2007, Harris 2007). In Pakistan, the species is listed as Critically Endangered (Sheikh and Molur 2005).