The complex gut microbiota plays a key role in host metabolism and health. However, the core microbial communities in the different aged Bactrian camels remain totally unclear. We used high-throughput 16S rRNA gene sequencing to examine the temporal variability of the fecal microbiota in Bactrian camels. At 2 months of age, the fecal microbiota was composed of Firmicutes, Proteobacteria, and Actinobacteria. At 1 and 3 years of age, the fecal microbiota was dominated by Firmicutes, Bacteroidetes, and Verrucomicrobia. At the genus level, Blautia, Fusobacterium, and Bifidobacterium were more abundant at 2 months of age, as well as Escherichia-Shigella. Ruminococcaceae_UCG-005, Akkermansia, and Christensenellaceae_R-7_group were the most abundant at 1 and 3 years of age. Diversity and stability of the gut microbiota increased with age. There was enrichment for genes associated with immune system diseases at 2 months of age. This study is the first to investigate the distribution of the gut microbiota in Bactrian camels with different ages and provide a baseline for future camel microbiology research.