The metabolic characteristics of Daqu are crucial factors affecting the sensory attributes of Baijiu. However, the mechanisms underlying the development of Daqu's metabolic profile, particularly the relationship with functional species, remain insufficiently understood. Therefore, we employed Qu-omics to comprehensively analyze the metabolic profiles of the three typical types of Daqu, namely high-, medium-, and low-temperature Daqu (HTD, MTD, and LTD). Flavoromics and metabolomics analyses revealed that the concentrations of both volatile and non-volatile compounds were highest in MTD, followed by those in LTD, which were characterized by elevated levels of esters, alcohols, and organic acids. In contrast, HTD exhibited a distinct metabolic profile, with a significantly higher abundance of aldehydes, ketones, pyrazines, amino acids, and small peptides. Additionally, 47 volatiles and 26 non-volatiles were identified as differential markers among three types of Daqu, including aroma-active compounds such as 2,5-dimethylpyrazine and phenethyl alcohol. The metabolic pathways associated with these metabolites were reconstructed by integrating metagenomic datasets, which highlighted the potential role of functional bacteria in shaping Daqu's metabolic profiles. Specifically, Staphylococcus gallinarum, Brevibacterium intestinavium, and Kroppenstedtia eburnean may play essential roles in HTD, while Bacillus velezensis/Weissella cibaria and Kosakonia cowanii/Pantoea agglomerans in MTD and LTD, respectively. These findings enhance our understanding of the metabolic diversity of Chinese Daqu and provide valuable insights for flavor regulation.