s: To investigate the origin of microbial sources of fermented grains in multiple stages of Taorong-type Baijiu and the role of multiple production environments in contributing to the microbiota of fermented grains. In this study, we used single-molecule real-time sequencing to investigate the microbial community structure of grains, Jiuqu, and brewing environments (air, tools, etc.) in a multi-stage fermentation, as well as microbial traceability of the fermented grains.The results showed that, at the species level, the microbiota species of fermented grains did not change significantly before and after stacking, and community succession occurred only in terms of species richness. The composition and abundance of microorganisms of fermented grains changed significantly after 7 days of fermentation in the cellar. A traceability analysis revealed that the microbial communities of fermented grains before and after stacking were primarily derived from Fuqu, medium-temperature Daqu, and production tools. After 7 days of fermentation in the cellar, pit mud, the production floor, and tools became the primary contributors to the microbiota of the fermented grains. Furthermore, the spearman correlation network found that the interaction between microorganisms from jiuqu and the environment drives the succession of microbial community structure in fermented grains. This study provides new insights into the origin and structure formation of fermented grains microbial communities at different periods, as well as provides an efficacious reference for quality control and standardized production of Baijiu and other traditional fermented foods.