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Simple Summary: The intestinal microbiome structure and diversity of Alpine musk deer in Gansu (origin) and Sichuan (migration) were analyzed in this study using 16S rRNA high-throughput sequencing technology. The study revealed that there were no alterations in the dominant intestinal species between musk deer in the origin and migration areas. However, there were significant differences in their relative abundance. Therefore, specific measures should be implemented for the feeding and management of migratory Alpine musk deer. This study provides a theoretical foundation for expanding artificial populations and reintroducing wild populations. In China, the population of wild musk deer, belonging to the family Moschidae, has drastically decreased in recent years owing to human activities and environmental changes. During the 1990s, artificial breeding of Alpine musk deer was conducted in Xinglong Mountain, Gansu Province, China, and their ex situ conservation was explored for over a decade. Ex situ protection is beneficial for expanding the population of animals and maintaining their genetic diversity; however, it can also induce metabolic diseases and parasitic infections and reduce reproductive capacity. The gut microbiota of animals has a considerable impact on host energy metabolism and immune regulation, thereby playing a crucial role in the overall health and reproductive success of the host. In this study, by comparing the differences in the intestinal microbiome of the musk deer according to their place of origin and migration, the changes in their gut microbiota and the influencing factors were explored to provide a theoretical basis for monitoring the health status of the musk deer. We used 16S rRNA high-throughput sequencing technology to analyze the structure and diversity of the gut microbiota of Alpine musk deer in Gansu (G, place of origin) and Sichuan (S, place of migration). The results showed that the dominant bacteria and genera in the intestinal microbiome of captive musk deer were similar in the places of origin and migration, but significant differences were observed in their relative abundance (p < 0.05). Regarding Firmicutes and Actinobacteria, which are related to plant cellulose digestion, the relative abundance in group G was higher than that in group S; regarding Proteobacteria and Verrucomicrobia, which are related to fat and starch intake, the relative abundance in group S was higher than that in group G; the relative abundance of Bacillus and Clostridium sensu stricto, which are related to fiber digestibility, was higher in group G than in group S; the relative abundance of conditional pathogens Acinetobacter and Escherichia–Shigella was higher in group S than in group G. The results of α and β diversity analysis also showed significant differences between the two groups (p < 0.05). The ACE and Shannon indices of musk deer in group G were considerably higher than those in group S, and the Simpson index of musk deer in group S was greater than that in group G, indicating that the abundance and diversity of intestinal microbiome were higher in musk deer of Gansu than those of Sichuan. Comparison of the changes in the intestinal microbiome of the musk deer according to the place of origin and migration showed that the plant cellulose content in the food of the musk deer, the fat content in the concentrated feed, and changes in the feeding environment have an impact on the intestinal microbiome. Effective monitoring of the health and immunity of the musk deer is crucial for ensuring their overall health, which in turn will aid in formulating a scientific and reasonable management plan for their conservation. [ABSTRACT FROM AUTHOR]