BACKGROUND: Ulcerative colitis (UC) is a chronic disease that induces colon tissue damage. Previous studies have shown the clinical benefit of New Baitouweng Decoction (NBD). Here, we aimed to investigate the effects of NBD on dextran sodium sulfate (DSS)-induced UC and the underlying mechanisms in a mouse model. METHODS: UC was induced in mice by using DSS for 7 days. The efficacy of NBD was determined by analysing the pathological appearance and the expression of inflammatory factors and tight junction proteins. 16S rDNA sequencing was used to describe the gut microbiota. Gas chromatography-mass spectrometry was employed to quantify bile acid (BA) levels. Spearman's correlation analysis was conducted to determine the relationship between gut microbiota composition and BA profiles. Western blot was used to detect the amounts of farnesoid X receptor (FXR), Nod-like receptor (NLR) family pyrin domain containing 3 (NLRP3), caspase-1, and cleaved caspase-1. RESULTS: NBD reduced the disease activity index scores, ameliorated colonic pathological damage, inhibited colon inflammation, and repaired the intestinal barrier. In addition, 16S rDNA sequencing showed that NBD enhanced the relative abundance of beneficial bacteria such as Lactobacillus and Akkermansia, known to be involved in fecal BA metabolism. Furthermore, BA metabolomics analysis indicated that NBD elevated the concentrations of lithocholic acid and deoxycholic acid, thereby linking to the activation of the FXR pathway to inhibit NLRP3-mediated inflammation. Inhibiting FXR activation by using Z-guggulsterone impeded the protective function of NBD in DSS-induced UC. CONCLUSION: NBD had a therapeutic effect on DSS-induced UC in a mouse model by regulating the gut microbiota, BAs, and subsequent FXR-NLRP3 pathway for decreasing the release of pro-inflammatory factors and repairing the intestinal barrier to preserve the equilibrium.