Daqu, a crucial fermentation starter for Chinese Baijiu, develops distinct microbial and physicochemical profiles depending on fermentation temperature, which significantly influence enzymatic activity and flavor formation. While high-temperature (HT-Daqu, 65 °C) and medium-temperature (MT-Daqu, 60 °C) variants are known to produce different liquor aromas, systematic comparisons of their microbial and physicochemical dynamics remain limited. This study integrated physicochemical assays (moisture, starch, acidity, enzymatic activity) with 16S rRNA and ITS (Internal Transcribed Spacer) sequencing to analyze HT-Daqu (HQ1–HQ3) and MT-Daqu (MQ1–MQ3) from Sichuan breweries. Results revealed that HT-Daqu exhibited significantly lower moisture (p < 0.05) and starch content (p < 0.05) but higher acidity (p < 0.05) compared to MT-Daqu. Enzymatic activities were generally reduced in HT-Daqu, except for neutral protease. Microbial profiling revealed distinct microbial dynamics between HT-Daqu and MT-Daqu: HT-Daqu harbored thermophilic Bacillus (40–60% relative abundance) with reduced fungal diversity, while MT-Daqu prioritized fungal consortia—Aspergillus dominated MQ1 (78%) and Saccharomyces transiently peaked in MQ2 (35%)—which correlated with enhanced saccharification enzyme activities and esterification potential. Alpha-diversity indices confirmed higher bacterial diversity in HT-Daqu and greater fungal richness in MT-Daqu. Correlation networks highlighted temperature-driven linkages, such as Bacillus positively associating with acidity. These findings elucidate the trade-offs between microbial stress adaptation and metabolic efficiency under different thermal regimes, providing actionable insights for optimizing Daqu production through targeted microbial management and temperature control to enhance liquor quality.

This study examines the effects of artificial and mechanical production on the physicochemical properties, enzyme activities, flavor components, and microbial diversity of medium-high temperature Daqu, a crucial starter culture for Chinese Baijiu. The research aims to elucidate how these production methods influence the quality of Daqu and to provide technical insights for optimizing industrial production processes. Results demonstrate that artificial Daqu exhibits 0.24% higher reducing sugar content (p < 0.05), 8.3% greater water retention (p < 0.01), and a 0.10-unit increase in acidity (p < 0.05) compared to mechanically produced Daqu. In contrast, mechanically produced Daqu displays a greater liquefaction capability but reduced fermentation capacity. An analysis of volatile flavor compounds reveals that artificially produced Daqu contains a broader spectrum of aroma compounds, particularly esters and alcohols, which are critical for the flavor profile of Baijiu. Microbial analysis demonstrates that artificially produced Daqu possesses a richer diversity of bacterial and fungal communities, with dominant genera such as Aspergillus, Saccharomyces, and Lactobacillus playing a pivotal role in flavor development. These findings offer valuable insights for optimizing Daqu production methods, balancing traditional craftsmanship with modern industrial demands to ensure consistent quality and flavor in Baijiu production.