Abstract: Based on the synergistic potential of microbial fermentation technology in enhancing the efficacy of medicinal and edible homologous substances, this study investigated the effects of compound microbial fermentation on bioactive components and flavor profiles of Pueraria lobata, Penthorum chinense, and Hovenia dulcis. Through combined enzymatic hydrolysis (cellulase) and microbial fermentation (Lactobacillus, Acetobacter, yeast), dynamic changes in bioactive compounds, functional activities, and flavor characteristics were systematically analyzed. Results demonstrated that enzymatic hydrolysis significantly increased the content of active compounds such as puerarin (250.43 μg/mL) and afzelin (44.34 μg/mL) (P<0.05), while generating epicatechin (41.16 μg/mL). During fermentation, macromolecules like flavoskyrin A were degraded. Total phenolic content (TPC) and total flavonoid content (TFC) exhibited an initial decline followed by an upward trend. The enzymolysis-fermentation (M7D) group showed superior ferric ion reducing antioxidant power (76.00 μg TE/mL) and DPPH radical scavenging capacity (IC₅₀=0.2447 mg/mL), significantly outperforming control and other experimental groups (P<0.05), though its ABTS⁺· scavenging capacity was relatively weaker (IC₅₀=0.3022 mg/mL). Notably, the M7D group retained effective α-glucosidase inhibitory activity (IC₅₀=0.0898 mg/mL). Volatile component analysis revealed: Compared to the control group, substantial increased in alcohols (increase of 299.23% and 230.89%, respectively), aldehydes (increase of 237.78% and 207.02%, respectively), and esters (increase of 51.86% and 46.29%, respectively) in fermented groups (S7D and M7D) (P<0.05). Core aroma compounds, including β-ionone (fruity/floral), phenethyl alcohol (floral/honey), and isoamyl acetate (fruity), synergistically enhanced olfactory complexity. Sensory evaluation indicated that the M7D group achieved optimal flavor integration, balancing herbal characteristics with moderate fermentation acidity, eliminating astringency, and harmonizing medicinal and fermented aromas. This research provides theoretical support for developing fermented beverages with dual antioxidant and flavor-enhancing properties.