Abstract: Mastering the indigenous microbial community structure and function in in-situ coal seams is an effective way to explore and control the biotransformation of in-situ coal seams. In order to accurately reflect the in-situ flora, newly exposed coal samples at different burial depths were collected using geological drilling. Through 16S rRNA and 18S rRNA high-throughput sequencing, the Alpha diversity, community composition and differences of the bacterial, archaeal and fungal communities in in-situ coal samples were analyzed. Finally, secondary function prediction was performed based on KEGG and MetaCyc databases. In the in-situ coal samples, the microbial community richness decreased with increasing of coal sample burial depth. Among them, bacteria identified 27 phyla, 67 classes, 159 orders, 267 families and 468 genera, with Proteobacteria and Aquabacterium as the dominant phyla and genera. Archaea identified 6 phyla, 14 classes, 21 orders, 26 families and 31 genera. The dominant phyla of archaea were Euryarchaeota, Asgardaeota and Crenarchaeota, and methanobacterium was found among the dominant genera. The fungal community obtained 20 phyla, 38 classes, 52 orders, 66 families and 72 genera; the dominant phyla of fungi included the Streptophyta, Ascomycota and Colpodellidae, and the dominant genera were Zea, Colpodella and Saccharomycopsis. The main functional prediction of microbial communities was the metabolism of substances and energy required to maintain basic microbial life activities. The research results will provide a reference for the preferential selection of coalbed methane bioengineering blocks.