Background <p>Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease with a globally increasing incidence. <i>Faecalibacterium prausnitzii</i> (<i>F. prausnitzii</i>) is known for its anti-inflammatory and immunomodulatory properties. However, the mechanisms by which gut microbiota and bile acid metabolism contribute to the therapeutic effects of <i>F. prausnitzii</i> in colitis remain unclear.</p> Aims <p>This study aims to investigate the effects of <i>F. prausnitzii</i> on colitis and elucidate its potential mechanism through modulation of gut microbiota and bile acid metabolism.</p> Methods <p>Mice were treated with dextran sulfate sodium (DSS), followed by administration of <i>F. prausnitzii</i> and its supernatant. Colitis symptoms, inflammatory responses, and intestinal barrier integrity were then evaluated. 16S rRNA sequencing and targeted bile acid metabolomics analysis were performed.</p> Results <p><i>F. prausnitzii</i> and its supernatant reshaped dysbiotic gut microbiota in DSS-induced colitis mouse models, increasing the ratio of unconjugated to conjugated bile acids and secondary to primary bile acids, thereby activating the farnesoid X receptor (FXR) signaling pathway. Experiments in FXR^−/− mice confirmed that FXR is a critical target for the protective effects of <i>F. prausnitzii</i>, promoting intestinal mucosal repair and inhibiting NLRP3 inflammasome activation, which in turn alleviates colitis. Additionally, the differential bile acid isoLCA, enriched by <i>F. prausnitzii</i> and its supernatant, effectively suppressed inflammation and enhanced intestinal barrier function.</p> Conclusion <p>This study demonstrates that <i>F. prausnitzii</i> alleviates colitis by modulating bile acid composition and regulating FXR signaling, suggesting that targeting the microbiota–bile acid–FXR pathway may represent a promising therapeutic strategy for inflammatory bowel disease.</p>