Inhabiting mountainous taiga (broadleaf and needle forest), these animals are typically found in forests of dense birch (Betula spp.) and larch (Larix spp.), and shrub-covered slopes in sub-alpine zones (Dulamtseren 1977, Dulamtseren et al. 1989, Tsendjav 2002). In Russia it inhabits the mid-mountain belt where it prefers dark coniferous forest with dense shrubs and rocky outcrops, using such rocky areas to escape from predators (Prohod’ko 2002). However, lichens are the main part of Siberian Musk Deer diet, accounting for up to 99% of the food intake in winter. During the rest of the year the percentage of lichen in the diet is still high, but these deer also consume grasses, leaves and mushrooms. When feeding it is able to climb on inclined trunks up to 3-4 m above ground. Population density is highly correlated with the availability of food and hiding places. The average population density is about 0.6 animals per square kilometre, although under favourable conditions this may be as high as 4-8.5 animals per square kilometre (Prohod’ko 2002). It has a thick coat for insulation and is well adapted for walking through deep snow. The species is preyed upon by a suite of predators including lynx, wolverine, yellow-throated marten, and rarely wolf, tiger, and bear. When chased, musk deer head for rocky terrain, and will try to reach an inaccessible crag or a shelter. If neither is available, the animal begins to run in circles. Although they can run exceptionally fast, musk deer tire after only 200-300 metres.

It is solitary, though it sometimes occurs in small groups (no more than three individuals) of a female with her young. In the Altai, family groups consist usually of an adult permanent pair and the young of the year. The territory of female and young lies within the territory of a male. Sometimes the group includes young males up to two years old, that are submissive to the adult male, but actively participate in making and protecting common territory (Prohod’ko 2002). The species is primarily active at dusk and dawn. While foraging, a musk deer may travel 3-7 km per night, generally returning to the same spot (a "lair") every morning. Individuals inhabit home ranges between 200 and 300 hectares in size, sticking to the boundaries steadfastly. The size of the home range decreases markedly during the second half of winter. Seasonal migrations are minimal if present at all. Reproduction starts in December, although some females do not mate until March (Prohod’ko 2002). Females gestate for just over 6 months, and give birth to 1-3 offspring, usually in May or June. Young wean at 3-4 months, and are mature at 15-17 months. Animals live in the wild for 10-14 years.

This species occurs widely in the Russian Federation (Siberia and the Far East), extreme eastern Kazakhstan, northeastern and northwestern China, Mongolia, Republic of Korea and Democratic People's Republic of Korea (Tsendjav 2002). Records from Afghanistan, Pakistan, India, Kyrgyzstan, Nepal, Bhutan, Myanmar and Viet Nam refer to other species in the genus Moschus. Four subspecies occur in Russia: M. m. moschiferus (Siberia); M. m. turovi (Russian Far East); M. m. arcticus (Verkhoyansk Ridge); and M. m. sachalinensis (Sakhalin Island). In Mongolia, M. m. moschiferus is found regionally in the forested habitats in the northern Mongol Altai mountain range (Togtokhbayar et al., 2000), Hangai mountain range (Sosorburam 1970, Dulamtseren 1977, Dulamtseren et al. 1989), Hentii and Hövsgöl mountain ranges, and possibly around Han Höhii Mountain in the western Hangai mountain range (Dulamtseren et al. 1989, Wemmer 1998, Tsendjav 2002). Two subspecies are found in China: M. m. moschiferus in Xinjiang (Altai mountains), Nei Mongol, and Heilongjiang; and M. m. parvipes along the border with North Korea in the Lesser Xing’an and Changbai mountain ranges, as far west as Ordos Plateau. M. m. parvipes occurs widely in both North and South Korea.

This species is listed under CITES Appendix II. The Sakhalin subspecies (M. m. sachaliensis) is listed in Red List of Russian Federation as Category I (Critically Endangered). It is protected as Very Rare under part 7.1 of the Law of the Mongolian Animal Kingdom (2000). Hunting in Mongolia has been prohibited since 1953, and it is protected as Very Rare under the 1995 Mongolian Hunting Law (MNE 1996). It is also on the 2014 Chinese Red List as Critically Endangered A1acd+B1ab(i, ii, iii), and is included on the China Key List - II.
In Russia it is present in a number of protected areas. Approximately 13% of the species’ range in Mongolia occurs within protected areas. More than 1.5 million hectares of the range of this species is included within Horgo Terkhiin Tsagaan Nuur National Park (Hangai Mountain Range), Hövsgöl Nuur National Park (Hövsgöl Mountain Range), and Gorkhi Terelj National Park, Bogd Khan Uul Strictly Protected Area, and Khan Hentii Strictly Protected Area in Hentii Mountain Range (Wemmer 1998).

The following conservation measures are needed through its range (Wang et al 1993, Wemmer et al 1998):

• Enhance enforcement of existing protective legislature, particularly relating to trade in musk through increased vigilance within protected areas and by customs agents at border crossings.
• Conduct further ecological research and monitor population trends, including on population dynamics, dispersal, and the effects of harvesting. No national surveys of Siberian musk deer population size have been conducted for over 30 years (Homes 2004).
• Regulate illegal logging and human-caused fires within its range (R. Reading pers. comm.).
• Organise a workshop including representatives from Mongolia, China, Russia and the Koreas to focus international efforts on conservation and to agree upon realistic yet effective solutions to threats faced by this species (Homes 2004).
• Identify substitutes for musk which would be acceptable in traditional forms of East Asian medicine (Homes 2004).

The species is successfully bred in captivity at musk deer farms, especially in Russia (in the Altai and Moscow regions) and China.