The fungal composition of medium-high temperature Daqu (MHTD) is one of the key factors determining the style of Baijiu. However, systematic research on the commonalities and differences of fungal communities across regions remains scarce. To systematically elucidate the common regularities and differentiation characteristics of the fungal community structure in cross-regional MHTD in China, high-throughput sequencing data of Daqu from Baijiu enterprises in five regions (Bayan Nur in Inner Mongolia, Linyi in Shandong, Zhoukou in Henan, Weifang in Shandong, and Yingtan in Jiangxi) were integrated in this study, and their fungal compositions and interactions were comparatively analyzed. The analysis revealed that Thermomyces (22.11%), Rhizopus (15.89%), and Aspergillus (14.68%), among others, constituted the dominant fungal genera. Furthermore, Rhizopus, Aspergillus, and others formed a shared core fungal community across all regions, accounting for 67.64%–83.15% of the total abundance. LEfSe analysis clarified the significantly enriched characteristic fungal taxa in each region, such as Thermomyces in Bayan Nur and Pichia in Linyi. Correlation analysis revealed that complex fungal interaction networks were formed in the Daqu from Zhoukou (Henan) and the two regions in Shandong, while multiple interactions, such as the positive correlation between Apiotrichum and Trichosporon, exhibited cross-regional stability. Overall, the fungal communities of MHTD from the five regions exhibited an ecological characteristic characterized by the coexistence of core taxa conservation and regional specificity. This study establishes a microbiological foundation for elucidating the formation mechanisms of unique Baijiu flavors in enterprises across various regions.