This study investigates the microbial community in three-color sauce-flavor Daqu (black, yellow, and white) during their maturation processes, along with physicochemical factors, cultivable microbes, flavor components, and fermenting vitalities. High-throughput sequencing revealed distinct microbial diversity, with more pronounced variations in bacterial communities than in fungal communities. Firmicutes and Ascomycota were the dominant bacterial and fungal phyla, respectively. Kroppenstedia, Virgibacillus, and Bacillus were the most dominant bacteria in black, yellow, and white Daqu, respectively, while Thermoascus was the core dominant fungus for all three types. Physicochemical factors, particularly acidity, significantly influenced the microbial community. Kroppenstedia played a key role in color formation through the Maillard reaction. Molds (Aspergillus, Rhizomucor, and Rhizopus) contributed significantly to the formation of pyrazine compounds. The study provides insights into the microbial perspectives on color and pyrazine formation, laying a foundation for future mechanized Daqu production and quality control in sauce-flavor baijiu brewing.This study investigates the microbial community in three-color sauce-flavor Daqu (black, yellow, and white) during their maturation processes, along with physicochemical factors, cultivable microbes, flavor components, and fermenting vitalities. High-throughput sequencing revealed distinct microbial diversity, with more pronounced variations in bacterial communities than in fungal communities. Firmicutes and Ascomycota were the dominant bacterial and fungal phyla, respectively. Kroppenstedia, Virgibacillus, and Bacillus were the most dominant bacteria in black, yellow, and white Daqu, respectively, while Thermoascus was the core dominant fungus for all three types. Physicochemical factors, particularly acidity, significantly influenced the microbial community. Kroppenstedia played a key role in color formation through the Maillard reaction. Molds (Aspergillus, Rhizomucor, and Rhizopus) contributed significantly to the formation of pyrazine compounds. The study provides insights into the microbial perspectives on color and pyrazine formation, laying a foundation for future mechanized Daqu production and quality control in sauce-flavor baijiu brewing.