This study investigated the hepatoprotective effects of Cortex Fraxini (CF), focusing on the interaction between its antibacterial constituents and gut microbiota. In vitro fermentation of CF extract with rat fecal bacteria led to changes in the content of four typical coumarins (fraxin, fraxetin, esculin, and esculetin) and produced a metabolite (labeled as mCoumarin). Fraxetin exhibited potent antibacterial and anti-inflammatory activities, whereas mCoumarin, despite its milder direct effects, notably increased the prebiotic index and promoted the growth of beneficial bacteria, such as Lactobacillus. In vivo experiments using a CCl4-induced liver injury mouse model demonstrated that mCoumarin significantly improved liver function, as evidenced by reduced levels of serum AST, ALT, TBIL, and MDA, and increased levels of antioxidant enzymes SOD and GSH-PX. Additionally, mCoumarin decreased the levels of the pro-inflammatory cytokines IL-6, IL-1β, and TNF-α, indicating a reduction in liver inflammation. Analysis of the gut microbiota revealed that mCoumarin maintained the relative abundance of several beneficial bacteria, suggesting a crucial role in preserving the gut microbial balance. This study revealed that mCoumarin, the terminal metabolite of CF coumarin, is a promising candidate for hepatoprotection, potentially through its ability to modulate the gut microbiota and gut-liver axis. This study advances our understanding of the mechanisms underlying the hepatoprotective effects of CF and underscores the potential of targeting the gut microbiota in the development of novel therapeutic strategies for liver diseases.