Aims Microorganisms in fermentation pits (FPs) play key roles for Chinese-strong-aromatic-liquor (CSAL) production. However, the microbial community in the FPs is still poorly understood. Here, the aim of this study was to reveal the diversity and potential functions of microbiota in FPs. Methods and Results Sequencing-by-synthesis-based metagenomic sequencing and annotation results revealed that the microbiota of FPs was primarily composed of Firmicutes (54 center dot 6%), Euryarchaeota (15 center dot 3%), Bacteroidetes (10 center dot 1%), Gammaproteobacteria (5 center dot 8%), Opisthokonta (5 center dot 7%) and Unclassified_Bacteria (2 center dot 3%). And 133 genera were identified as the dominant genera of this fermentative food. Lactobacillus, Sedimentibacter, Syntrophomonas, Methanoculleus, Methanobacterium, Bacillus, Clostridium, Galactomyces, Candida, Pichia, Penicillium and Aspergillus were defined as active populations for biosynthesizing the characteristic volatile compounds of CSAL. The study also revealed that the microbial community structures changed significantly with different cellar ages and over different geographical regions. (i) The presence of Bacteroidetes was the most distinctive feature that characterized the different FPs ages. (ii) Distinct contents of Gammaproteobacteria and Euryarchaeota were observed at different positions in the FPs. (iii) Euryarchaeota markedly contributed to the generation of the character of the liquors with distinct geographical associations. Conclusions This study demonstrated that the changes of microbial communities determined the different quality characteristics of CSAL. Significance and Impact of the Study This research contributes to a deeper understanding of the FPs microbial composition and shows a new microbial resource for biotechnological applications.