This study employed metagenomics, flavoromics, and physicochemical analysis to elucidate the regulatory mechanism of different types of mother Daqu on fungal community succession, functional gene expression, and volatile compound dynamics during the fermentation of Daqu. The types of mother Daqu significantly affected the successional trajectory and stability of the fungal community. Specifically, mother Daqu for yellow Daqu maintained a stable consortium dominated by Aspergillus, Ramsonia, and Talaromyces, resulting in high community homogeneity. In contrast, mother Daqu for black and white Daqu showed significant fungal community shifts. Furthermore, both the abundance and taxonomic origin of the functional genes encoding carbohydrate-active enzymes (CAZy) and key flavor compounds (pyrazines and phenylethanol) were mother Daqu-specific. Random forest modeling pinpointed moisture as an important physicochemical factor influencing the fungal community. Path analysis further delineated the relationship of core fungi with key physicochemical factors and volatile substances. Our findings demonstrate that specific microbial consortia in mother Daqu drive fungal succession and metabolic functional differentiation, which in turn influence Daqu quality. This work provides a practical foundation for optimizing the fermentation process and selecting excellent mother Daqu.