[Objectives]  To compare the microbial community composition and function of Hepialus baimaensis Liang and H. yunnanensis Yang, Li et Shen, and to investigate the influence of the microbial community on the infection of H. baimaensis by Ophiocordyceps sinensis (Berk.) Sung et al.. [Methods]  The microbial 16S rRNA and internal transcribed space (ITS) of 4th and 5th instar larvae of H. baimaensis and H. yunnanensis were sequencing using the Ion S5^TMXL high-throughput sequencing method. The community composition of these species, LefSe (LDA effect size), predicted community function and comparative analysis of bacteria and fungi, were carried out using bioinformatics analysis software. [Results]  Seventeen phyla and 145 genera of bacteria were identified in H. baimaensis, and 23 phyla and 202 genera in H. yunnanensis. In H. baimaensis, 95.55% of bacteria species belonged to the dominant genera Carnobacterium, whereas Wolbachia was the dominant genera (85.28%) in H. yunnanensis. Four phyla and 114 fungal genera were identified in H. baimaensis, and 5 phyla and 113 genera in H. yunnanensis. Pseudogymnoascus was dominant fungal genera (46.23%) in H. baimaensis, whereas Mycocentrospora was the dominant genera (37.87%) in H. yunnanensis. LefSe analysis indicates that the 5 bacterial taxa and 12 fungal taxa found in H. baimaensis were significantly different to those found in H. yunnanensis. The 7 bacterial taxa and 9 fungal taxa in H. yunnanensis were also significantly different to those in H. baimaensis . COG analysis of the bacterial communities indicates that most bacteria are involved in amino acid transport and metabolism in H. baimaensis, whereas most are involved in translation, ribosomal structure and biogenesis in H. yunnanensis. Bacterial KEGG function predicted that the most common microbial functions were associated with DNA helicase, the ATP-binding cassette and ABC transporters in H. baimaensis, and with NADH: Ubiquinone reductase (H (+)-translocating), putative transposase and ribosome in H. yunnanensis. A FUNGuild analysis of fungal community indicates that 46.26% of all fungi originated from animal pathogen-soil saprotrophs in H. baimaensis. However, in H. yunnanensis, 38.31% of fungi originated from plant pathogens. KEGG and MetaCyc pathway function prediction indicates that the majority of fungi are related to basic metabolic, or physiological, functions. [Conclusion] The bacterial and fungal communities of 4th and 5th instar H. baimaensis and H. yunnanensis larvae were entirely different and there were also some differences in the functions of these communities between species. The bacterial and fungal communities of H. baimaensis larvae were the same as those of other hosts of O. sinensis, whereas the corresponding communities in H. yunnanensis were not. Carnobacterium and Pseudogymnoascus were, respectively, the dominant bacterial and fungal genera in H. baimaensis, and could play important roles in both larval growth and development, and in infection by O. sinensis.