Organic acids are essential constituents of bran vinegar, significantly influencing its sensory quality and functional characteristics. However, until now, little has been known about organic acid synthesis in bran vinegar. This study investigated the main physicochemical properties, organic acid composition, and changes in microbial diversity throughout the fermentation of Sichuan bran vinegar. Additionally, the functional microorganisms related to organic acid synthesis were analyzed. The results showed the presence of eight organic acids in bran vinegar. Amino acid nitrogen, reducing sugars, and alcohol content were identified as the main physicochemical factors contributing to organic acid formation. The dominant microorganisms associated with organic acids during fermentation included Lactobacillus, Acetobacter, Bacillus, Alternaria, Pichia, and Candida. Microbial communities related to specific organic acids during the fermentation of vinegar grains were identified using the two-way orthogonal partial least squares (O2PLS) model. Bacterial communities showed stronger correlations with the principal organic acids. These findings provided the basis for analyzing the formation of flavor compounds in the bran vinegar fermentation process.