Based on the 23 strains of low-temperature Daqu, microbial inoculants were prepared and inoculated into crushed barley and pea to prepare clean low-temperature Daqu (XQ). The physicochemical properties, flavor profile, and microbial community of XQ were investigated, with traditional low-temperature Daqu (CQ) and production requirements as controls. The results indicated that there was no significant difference in moisture and acidity between the two types of Daqu: CQ exhibited a moisture of 10.6% and an acidity of 1.1 mmol/10 g, while XQ demonstrated a moisture of 10.9% and an acidity of 1.2 mmol/10 g. The fermenting activity (1.36 g/0.5 g·72 h) and liquefying activity (1.13 g/g·h) of XQ surpassed those of CQ; however, its saccharifying activity (780 mg/g·h) and esterifying activity (808 mg/50 g·7 d) were lower. In general, the physicochemical properties of XQ align with the production requirements. HS-SPME-GC-MS analysis indicated that the flavor profiles of the two types of Daqu were largely similar, with 84.85% of the flavor components of CQ being reproducible in XQ. Microbiota community analysis revealed there were some differences in relative abundance of microbes and COG (Clusters of Orthologous Groups) function between the two Daqu. The dominant microorganisms in XQ identified were Bacillus, Pichia, Transversalis, and Monascus, meanwhile the dominant microorganisms in CQ identified were Pediococcus, Rhizomucor, Wickerhamomyces. This study establishes a robust experimental basis for producing clean Daqu and provides valuable insights for the development of safer microbial fermented foods.