This study aims to understand the development and succession of the microbial community during the production of traditional Aspergillus-type Douchi as well as their effects on the formation and variation of characteristic aroma compounds. High-throughput sequencing technology, solid-phase microextraction, gas chromatography–mass spectrometry, and Spearman correlation analysis were conducted to study the changes in the microbial community and characteristic flavor during the fermentation process. Aspergillus spp. was dominant in the early stage of fermentation, whereas Staphylococcus spp., Bacillus spp., and Millerozyma spp. became dominant later. At the early stage, the main flavor compounds were characteristic soy-derived alcohols and aldehydes, mainly 1-hexanol, 1-octen-3-ol, and nonanal. In the later stage, phenol, 2-methoxy-, and 3-octanone were formed. Correlation analysis showed that six bacterial genera and nine fungal genera were significantly correlated with the main volatile components, with higher correlation coefficients, occurring on fungi rather than bacteria. Alcohols and aldehydes were highly correlated with the relative abundance of bacteria, while that of yeast species such as Millerozyma spp., Kodamaea spp., and Candida spp. was positively correlated with decanal, 3-octanol, 2-methoxy-phenol, 4-ethyl-phenol, 3-octanone, and phenol. The novelty of this work lies in the molds that were dominant in the pre-fermentation stage, whereas the yeasts increased rapidly in the post-fermentation stage. This change was also an important reason for the formation of the special flavor of Douchi. Correlation analysis of fungi and flavor substances was more relevant than that of bacteria. As a foundation of our future focus, this work will potentially lead to improved quality of Douchi and shortening the production cycle by enriching the abundance of key microbes.