This study aims to investigate the effect of Coptidis Rhizoma-Zingiberis Rhizoma (CR-ZR) on gut microbiota and endogenous metabolites in mice with ulcerative colitis (UC) induced by dextran sodium sulfate (DSS). The principal active constituents of CR-ZR were determined via high-performance liquid chromatography (HPLC) analysis. Male C57BL/6 mice were randomly assigned to six groups: control, model, sulfasalazine (125 mg/kg), low-dose CR-ZR (22.5 mg/kg), medium-dose CR-ZR (45 mg/kg), and high-dose CR-ZR (90 mg/kg), with 10 mice in each group. To establish the UC model, all groups except the control were given 2.5% DSS in drinking water and subjected to gavage treatment for 11 days. Daily records of changes in body weight, fecal characteristics, and occult blood were maintained to determine the disease activity index (DAI). HE staining was used for colonic histological evaluation. The levels of cytokines including tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), IL-8, IL-4 and IL-10 were measured using ELISA. Furthermore, the gut microbiota was analyzed through 16S rRNA sequencing, and widely targeted metabolomic analysis was performed using UPLC-MS. Compared with the model group, the results indicated that CR-ZR treatment significantly reduced DAI scores (P＜0.01), colonic histological damage, and inflammatory cell infiltration in colitis mice. Serum levels of pro-inflammatory cytokines (TNF-α, IL-6 and IL-8) significantly decreased, whereas anti-inflammatory cytokine levels (IL-4 and IL-10) were markedly elevated (P＜0.01). 16S rRNA gene sequencing indicated that the Bacteroidota/Firmicutes ratio and the relative abundances of Alloprevotella, Lachnoclostridium, Mucispirillum, and Blautia in mice treated with CR-ZR suggested a trend towards a healthier state. Metabolomic analysis identified 20 biomarkers associated with the regulatory effects of CR-ZR, primarily involved in arginine biosynthesis and tryptophan metabolism pathways. These findings indicate that CR-ZR ameliorates UC by remodeling the disordered gut microbiota and regulating arginine biosynthesis and tryptophan metabolism.