Ulcerative colitis (UC) is a chronic inflammatory bowel disease in which dysbiosis of the intestinal flora plays a critical role in its pathogenesis. Polygonum hydropiper L-Coptis chinensis Franch (PH-CC) known for its anti-inflammatory properties and ability to regulate gut microbiota, has been demonstrated to alleviate UC. The aim of this study was to investigate the effects of PH-CC on dysbiosis of intestinal flora and metabolic disorders in dextran sodium sulfate (DSS)-induced UC mice. A UC mouse model was induced using a 3% DSS solution, and histopathological changes in the colon were assessed through hematoxylin and eosin staining. The composition and diversity of the intestinal flora were analyzed using 16S rDNA technology, whereas metabolomics was employed to identify potential differential metabolites and metabolic pathways through multivariate statistical analysis. Pearson correlation analysis was performed between metabolites, inflammatory factors, the NLRP3/Caspase-1 pathway, and differential flora. The results revealed that treatment with PH-CC improved the morphological structure of colon tissue and reduced damage in UC mice, while the model group exhibited significant damage to the crypt structure, exfoliation of the colonic mucosal epithelium, loss of glands, and infiltration of inflammatory cells. Analysis of 16S rDNA sequencing data indicated that PH-CC regulated the DSS-induced changes in gut microbiota, significantly decreasing the abundance of norank_f_norank_o_Rhodospirillales, norank_f_UCG-010, Corynebacterium, and Eubacterium_nodatum_group. The differential microbiota exhibited a strong correlation with the NLRP3/Caspase-1 pathway and downstream inflammatory factors. Additionally, 27 differential metabolites identified in fecal samples were primarily associated with phenylalanine metabolism and bile secretion, showing a high correlation with the differential microbiota. In conclusion, PH-CC regulates dysbiosis in intestinal flora and metabolic disorders in UC mice by reducing the abundance of specific bacterial groups, thereby alleviating inflammatory damage to the colonic mucosa and improving the overall condition of UC.