Abstract: This study aimed to systematically investigate the variation patterns of short-chain fatty acids (SCFAs) and the key microorganisms influencing their production during the brewing process of Sichuan Sun Vinegar. Gas chromatography and high-throughput sequencing were combined with multivariate statistical analyses to comprehensively characterize the SCFA contents and microbial community structures in Vinegar Pei during the aging stage. In conjunction with physicochemical parameters, redundancy analysis (RDA) was applied to elucidate the underlying driving factors. The results demonstrated that the aging stage represented a critical period for SCFA accumulation, during which the contents of isobutyric acid, butyric acid, and isovaleric acid increased most markedly (P<0.05), rising from 0.028, 0.032, and 0.061 mg/g to 0.073, 0.108, and 0.226 mg/g, corresponding to increases of 160.7%, 237.5%, and 270.5%, respectively. Several bacterial taxa, including Vibrionimonas, Chitinophaga, Labrys, and Methylobacterium–Methylorubrum, as well as fungal taxa such as Fusarium, Aspergillus, Rhodotorula, and Stachybotrys, were identified as potential functional microorganisms involved in SCFA production during the aging process. RDA further revealed that reducing sugars, total acid, and total phenols were key environmental factors driving the succession of these functional microbial communities. In conclusion, this study indicates that the accumulation of SCFAs during the aging of Sichuan Sun Vinegar is closely associated with specific microbial communities and is likely regulated by key physicochemical factors. These findings provide an important theoretical basis for the targeted regulation of Sun Vinegar flavor quality and for further elucidation of the biosynthetic mechanisms of SCFAs.