Musk Deer Moschus spp. is a wild animal under first class protection in China, and its artificial culture history has been more than 60 years. However, cultivation technology developed slowly due to inadequate feeding standards and nutritional requirements, as well as high morbidity and mortality. Researchers worked to solve these problems, but because Musk Deer is susceptible to environmental stress or pathological reactions, it is difficult to obtain representative test data and biological samples, and relevant studies have certain limitations. With the development of molecular biology technology, it is gradually found that intestinal microbiota is crucial to host health and plays a key role in host immune prevention and control, nutritional regulation and adaptive evolution. It is important to study the intestinal microbes to enrich relevant research and maintain the health of Musk Deer. Therefore, the composition, function and influencing factors of the bacterial-dominated intestinal microflora of Musk Deer were reviewed in this article, to provide a scientific reference for improving disease control and prevention, feeding management and nutritional regulation in the process of artificial Musk Deer farming.