Abstract: To investigate the impact of manual and mechanical methods of making high-temperature Daqu on the microbial community during storage, this study analyzed the differences in microbial community composition and succession patterns of Jiang-flavor Baijiui high-temperature Daqu made by manual and mechanical methods during the storage period (0-150 days) using Illumina MiSeq high-throughput sequencing technology combined with multivariate statistical analysis methods. Additionally, the bacterial functions and phenotypes were predicted based on BugBase. The results showed that the manual-made high-temperature Daqu had a significantly higher fungal community richness during storage compared to the mechanically-made Daqu (P<0.05), and the fungal community composition was also significantly different. However, there was no significant difference in bacterial community diversity between the two types of Daqu (P>0.05). Thermomyces was a key genus, but the dominant fungal genera varied with different storage times and Daqu-making methods. Lactobacillus was relatively enriched in the mechanical Daqu, while Bacillus was more prominent in the manual Daqu. Linear discriminant analysis revealed the impact of Daqu-making methods on biomarkers. Leptospora rubella and Trichomonascus ciferrii were the biomarkers for manual and mechanical Daqu at different storage periods, respectively. Weissella was the biomarker for the manual Daqu during storage, while Kocuria was the biomarker for the mechanical Daqu during storage. Moreover, different Daqu-making methods also had a significant impact on bacterial functions and phenotypes. Kroppenstedtia and Staphylococcus were the bacterial genera that were significantly positively correlated with multiple metabolic functions during the storage of manual and mechanical Daqu, respectively (P < 0.05). Both types of Daqu were dominated by Gram-positive bacteria, but the manual Daqu maintained a higher anaerobic bacterial activity phenotype. This study found that different Daqu-making methods have an impact on the microbial community structure, succession patterns, and bacterial functions and phenotypes during Daqu storage, providing a theoretical reference for the scientific regulation of Daqu storage and the analysis of the aging mechanism.