Medium-temperature Daqu acts as a fermentation starter for strong-flavor Baijiu. However, there is limited research available in terms of its quality attributes and formation mechanisms. In this study, the distinct characteristics of different quality medium-temperature Daqu were examined using the novel Qu-omics techniques. Multivariate statistical analyses indicated that the high-quality strong-flavor medium-temperature Daqu had increased acidity and enzyme activity, with the most significant variation observed in acidic protease activity. We revealed for the first time that mucorpepsin derived from Rhizomucor pusillus was the primary source of the acidic protease in high-quality Daqu using in-depth analysis. Volatile composition analysis revealed a positive correlation between nitrogenous and acidic substances with the predominant bacterial genera of Daqu, while a negative correlation was observed with the dominant fungal genera. The principal source of acidic compounds in Daqu was revealed to be lactic acid bacteria, and the inter-group differences in aromatic compounds were extremely significant (p < 0.001). The levels of phenylmethanol, phenylethanol, benzaldehyde, phenol, and 4-ethylguaiacol were significantly higher in high-quality Daqu compared to abnormal Daqu, while notably lower levels of phenylacetaldehyde, (±)-1-phenyl-2-propanol, phenylacetone, and other off-flavor substances were detected in high-quality Daqu than in abnormal Daqu (p < 0.05).