[Background] Fungus-growing termites are a kind of higher termites belonging to the family Macrotermitinae that cultivated monofungus (Termitomyces spp.) in their nest. Fungus-growing termites form a three-dimensional symbiosis system with intestinal microbes and microorganisms in the fungus garden. [Objective] To analyze the microbial diversity of fungus combs and termite feces, and compares with intestinal microbes of fungus-growing termites. [Methods] The bacterial 16S rRNA gene mplicon and fungal ITS rRNA analysis were performed by the Illumina MiSeq high-throughput sequencing method. [Results] The number of filtered sequences and OTU numbers of bacteria and fungi in samples of fungus comb and feces were obtained. The number of bacterial OTU in the five samples was between 90?199, while the fungal OTU was between 10?58. The diversity of bacteria was significantly greater than that of fungi. Both the number of OTU in bacteria and fungi in fecal samples are more than that in fungus comb samples. According to the analysis of taxa classification, the dominant phylum in the fungus comb samples are Proteobacteria, with a relative content of over 82.4%; followed by Bacteroidetes and Firmicutes; the dominant bacteria in fecal samples are Bacteroides, followed by Proteobacteria. The dominant bacteria belong to Alistipes and Dysgonomonas, which is consistent with the diversity of intestinal bacteria in fungus-growing termites. The dominant fungi in termite comb and fecal samples are mainly Basidiomycota and Ascomycota. The dominant fungi genus in fungus comb is Termitomyces, with a relative content of more than 51.83%. Xylaria is also identified in the comb. [Conclusion] This study provides a basis and reference for the future research on the symbiosis of fungus-growing termites with in vivo and in vitro microorganisms and the isolation and culture of microorganisms.