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 2months of age, the fecal microbiota was composed of Firmicutes, Proteobacteria, and Actinobacteria. At 1 and 3years of age, the fecal microbiota was dominated by Firmicutes, Bacteroidetes, and Verrucomicrobia. At the genus level, Blautia, Fusobacterium, and Bifidobacterium were more abundant at 2months of age, as well as Escherichia-Shigella. Ruminococcaceae_UCG-005, Akkermansia, and Christensenellaceae_R-7_group were the most abundant at 1 and 3years of age. Diversity and stability of the gut microbiota increased with age. There was enrichment for genes associated with immune system diseases at 2months 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.