This study investigated the effects of different methods of Bacillus inoculation (separate cultures, co-culture, and no inoculation) on the sensory characteristics and flavor pyrazine compounds of high-temperature Daqu. During the fermentation process, total acidity and moisture content decreased progressively, and sensory attributes of Bacillus-fortified Daqu were superior to those of the control group. For finished Daqu, the total content of pyrazine compounds was significantly higher in the experimental groups (3376.89 μg/g for fortified Daqu Ⅱ, 2842.47 μg/g for fortified Daqu Ⅰ) than in the control group (1868.78 μg/g). A total of 24 prokaryotic and 16 eukaryotic genera were identified as dominant microbiota. The abundance of Bacillus, Thermomyces, and Thermoascus in fortified Daqu was higher than that in the control group. A total of 21 prokaryotic and 19 eukaryotic differentially abundant microorganisms were identified. In summary, the inoculation of Bacillus seed culture contributed to improved sensory attributes, enhanced microbial diversity to some extent, and increased the concentration of pyrazine compounds, thereby improving the overall quality of high-temperature Daqu.