The unique quality of Baijiu, China's traditional distilled spirit, is intimately linked to its regional micro-ecology. However, the origins and assembly processes of these fermentation-relevant microbes in natural environments within major Baijiu production basins, like the upper Yangtze River, remain largely unexplored. This study comprehensively profiled the microbial communities (bacteria and fungi) across four habitats (water, soil, air, and plant surfaces) from 15 locations in the upper Yangtze River basin, a critical region for Baijiu production. Results indicated that habitat type was the primary factor shaping microbial structures. Notably, a core set of 30 microbial genera (14 bacterial and 16 fungal) with known functions in Baijiu fermentation was identified. These key taxa were predominantly enriched in the air and exhibited significant regional variation. Co-occurrence network analysis revealed higher structural complexity in river and plant soil communities, suggesting these as potential stability hubs for microbial resources. Community assembly was mainly governed by homogeneous selection, indicating deterministic environmental filtering. Our findings directly bridge environmental microbiology with food fermentation practices by mapping the distribution of functional brewing microbes. This work provides a crucial theoretical foundation for harnessing natural microbial resources to enhance Baijiu quality control, develop starter cultures, and ultimately support the sustainable development of the Baijiu industry.