Daqu is the fermenting starter in Chinese Baijiu brewing, contributing functional microorganisms, enzymes and flavor substances to the grain fermentation. Traditional daqu is produced in open environment where environmental factors and microbiota are critical to daqu and Baijiu quality. Mechanization is the direction of Baijiu production development. In this study, we investigated the mechanism of the effect of mechanized environment and manufacturing process on daqu production. Many functional microorganisms (e.g. Acetobacter, lactic acid bacteria and yeast) were distributed in the process environment, including indoor air, tube and equipment surfaces, which contributed to the initial bacterial/fungal composition in daqu (71.62%/28.47%) along with mature daqu powder (21.1%/61.65%). Our results also showed daqu microbiota formation was influenced by both stochastic and deterministic processes. The initial microorganisms produced large amounts of organic acids (19.24 g/kg) and bioheat (58.3 °C) during early fermentation stage, leading to a rapid temperature rise and water loss under the stacking process. Mature daqu powder mainly provided thermophilic microorganisms for fermentation stages during and after temperature rise, including Thermoactinomyces, Thermoascus, Thermomyces, Rhizomucor and Rhizopus, which produced enzymes and amino nitrogen for Baijiu fermentation, also ensuring stable microbiota among process batches. This work revealed the origin of the microbial community of strong-flavor daqu and showed that ecological environment suitable for daqu fermentation was created during the long-term continuous production process by adding mature daqu powder during daqu brick making and sprinkling it in the workshop, by which product quality was guaranteed.