Background <p>The host microbiota and hepatic drug-metabolizing enzymes are important mediators of the metabolism and biological effects of herbal components. Through bidirectional interactions, herbal medicines can also reshape the host microbial community. The clinical efficacy of Wendan Decoction (WDD) in treating metabolic dysfunction-associated fatty liver disease (MAFLD) has been well established. However, its interactions with the host microbiota through the gut-liver axis remain unclear.</p> Purpose <p>This study aimed to investigate the mechanism by which WDD modulates host microbial activity through the gut-liver axis to ameliorate MAFLD.</p> Methods <p>MAFLD models were established by high-fat diet (HFD) feeding and subsequently treated with WDD, <i>Parasutterella excrementihominis</i> (<i>P. excrementihominis</i>), or 7α-OH-T. The ABX group underwent antibiotic-mediated microbiota depletion before treatment. Multi-omics analyses were used to characterize the dynamic trajectories of microbiota-derived metabolites. These analyses included targeted bile acid (BA) profiling of serum, 16S rRNA gene sequencing and untargeted metabolomics of cecal contents, and proteomics and untargeted metabolomics of liver tissue. Hematoxylin and eosin, Oil Red O, and Alcian blue-periodic acid-Schiff staining were used to assess pathological changes in the liver and intestinal tissues during MAFLD. ELISA, Western blotting, and other assays were performed to quantify markers of inflammation and lipid metabolism. Following UPLC/UV detection of 7α-OH-T in portal vein serum, molecular docking and molecular dynamics simulations, together with cellular thermal shift assays (CETSA) and microscale thermophoresis (MST), were used to validate FXR as a target of 7α-OH-T.</p> Results <p>WDD alleviated hepatic steatosis, intestinal inflammation, and barrier dysfunction in MAFLD, but these effects depended on the integrity of the host microbiota. 16S rRNA gene sequencing showed that WDD promoted the growth of beneficial bacteria, including <i>Bacteroides</i> and <i>Parasutterella</i>. Combined analysis of targeted serum BA metabolomics and untargeted metabolomics of cecal contents indicated that WDD-mediated modulation of the host microbiota reduced the total serum BA load, increased alternative-pathway metabolites, including CDCA and TCDCA, in the liver and intestine, and decreased toxic secondary BAs, including DCA and LCA. Steroid and fatty acid metabolites, such as 7α-OH-T, were also increased. <i>Pearson</i> correlation analysis and <i>P. excrementihominis</i> transplantation experiments suggested that the increase in 7α-OH-T was closely associated with <i>P. excrementihominis</i>. Untargeted liver metabolomics and serological analyses confirmed that gut-derived 7α-OH-T entered the liver through the portal vein and acted on hepatic targets via the gut-liver axis. In animal experiments involving exogenous 7α-OH-T supplementation and in MAFLD THLE-2 cell models treated with 7α-OH-T, 7α-OH-T ameliorated hepatic lipid accumulation and promoted lipid utilization in THLE-2 cells. A series of interaction assays, including CETSA and MST, identified FXR as a target of 7α-OH-T. Furthermore, 7α-OH-T markedly activated the FXR/PPARα/CYP4A12A axis and served as a key messenger through which WDD-mediated regulation of <i>Parasutterella</i> alleviated MAFLD via the gut-liver axis.</p> Conclusions <p>WDD increased the abundance of <i>P. excrementihominis</i> and the level of the potentially associated metabolite 7α-OH-T. Through the portal circulation, 7α-OH-T promoted gut-liver crosstalk and targeted the FXR/PPARα/CYP4A12A axis, thereby ameliorating MAFLD.</p> Graphical Abstract <p></p>