BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease, the development of which is accompanied by dysregulation of bile acid metabolism. Abnormal bile acid accumulation in the intestine further exacerbates intestinal inflammation in patients with UC. Coptidis Rhizoma has potential therapeutic activity against UC; however, its capacity to modulate bile acids in UC remains poorly explored. PURPOSE: The objective of this study was to determine the therapeutic effects of epiberberine, one of the main alkaloids in Coptidis Rhizoma, on UC and elucidate its role in modulating bile acid homeostasis through intestinal FXR in alleviating UC. METHODS: The anti-inflammatory activity of epiberberine and its ability to activate intestinal FXR were validated in UC mouse and in vitro cell models. Binding interactions between epiberberine and FXR protein were determined using various techniques (CETSA, SIP, DARTS, IP-MS, and ITC). Molecular docking and site-directed mutagenesis analyzed key amino acid residues involved in epiberberine binding to FXR. Wild-type and Fxr(-/-) mice were employed to further validate the epiberberine target in vivo. RESULTS: Epiberberine activated intestinal FXR, enhancing the expressions of bile acid transporters (OSTalpha, OSTbeta, IBABP) and FGF15 secretion, a signaling molecule. This promoted the intestinal reabsorption of bile acids and inhibited their synthesis in UC mice, thus alleviating intestinal bile acid accumulation and the expression of inflammatory proteins (NF-kappaB, IL-1beta, IL-10, IL-6). Epiberberine could directly bind to FXR protein (K(D)=2.04 mumol/l), with MET265 and ARG331 identified as key binding sites between epiberberine and FXR protein. In Fxr-deficient mice, the regulatory effect of epiberberine on bile acids was abolished, which, in turn, reduced the ameliorative effect on UC. CONCLUSION: These findings indicate that UC is characterized by FXR inhibition and abnormal bile acid accumulation. Epiberberine ameliorates UC by activating ileal FXR to regulate bile acid enterohepatic circulation and alleviate bile acid accumulation in the intestines. Additionally, this study provides a new perspective for investigating mechanisms through which Coptidis Rhizoma alkaloids activate intestinal FXR to regulate bile acid homeostasis during UC therapy.