Polyphenols are important functional substances produced in the acetic acid fermentation (AAF) of Shanxi aged vinegar (SAV). Previous studies have shown that the metabolic activity of microorganisms is closely related to polyphenol production and accumulation. In this study, microorganisms in the AAF of SAV were analyzed to explore how to increase the polyphenol yield by changing the microorganisms and reveal the potential mechanism of the microbial influence on the polyphenol yield. Macrotranscriptome analysis showed that acetic and lactic acid bacteria dominated the AAF fermentation process and initially increased and decreased. Spearman correlation analysis and verification experiments showed that the co-addition of Acetobacter pasteurianus and Lactobacillus helveticus promoted the accumulation of polyphenols, and the total polyphenol content increased by 72% after strengthening.