This study aimed to investigate the mechanism of compound Agrimonia pilosula enteritis capsules (CAPEC) on ulcerative colitis (UC) in mice with dampness-heat syndrome. The mice were randomly divided into five groups: the control group, the model group, the positive drug (5-aminosalicylic acid, 5-ASA) group, the low-dose CAPEC (CAPEC-L) group and the high-dose CAPEC (CAPEC-H) group. The mice models were established by using high-fat high-sucrose diet, feeding with distilled spirit and dextran sulfate sodium (DSS). The effects of CAPEC on bile acids (BAs) metabolic profiles in bile and the FXR-SREBP-1 signaling pathway were investigated in the model of UC in mice with dampness-heat syndrome by ELISA, qRT-PCR, UHPLC-QQQ/MS, and histopathological analysis. The results showed that, compared with the model group, the CAPEC-L group and the CAPEC-H group significantly reduced the disease activity index (DAI), and proinflammatory cytokine levels (including IL-6, IL-1β, and TNF-α) in both serum and colon tissues. Additionally, CAPEC markedly ameliorated intestinal inflammation, hepatic lipid accumulation, and pathological alterations in tongue tissue. The CAPEC-H group significantly attenuated the abnormal elevation of BAs profiles in bile, and up-regulated hepatic mRNA levels of Cyp7a1, Cyp7b1, Cyp27a1, Bsep, Fxr, and Shp, while down-regulating Srebp-1 and Cyp8b1 expression. The experimental results suggest that CAPEC alleviates UC with dampness-heat syndrome by ameliorating BAs metabolic disorders, hepatic lipid accumulation, and intestinal inflammation. These findings provide mechanistic insights into CAPEC’s traditional effects of clearing heat and drying dampness, and strengthening the spleen to relieve diarrhea.