Objective To investigate the regulatory effect of Baitouweng Decoction on brain-gut peptides and inflammatory factors in a rat model of ulcerative colitis (UC). Methods A total of 62 rats were randomly divided into control group with 11 rats, model group with 11 rats, mesalazine group with 10 rats, and high-, middle-, and low-dose Baitouweng Decoction groups (with 10 rats in each group). The method of high-sugar high-fat drinking was used to establish a model of damp-heat syndrome, and all rats except those in the control group were induced with 2,4,6-trinitrobenzenesulfonic acid-ethanol to establish a model of UC. After successful modeling, the rats in the control group were given enema with 0.5 mL of normal saline, and those in each administration group were given enema with the corresponding drug 0.5 mL, once a day for 7 consecutive days. Body weight, stool form, and disease activity index (DAI) score were compared between groups; HE staining was used to observe histopathological changes of the colon; immunohistochemistry was used to measure the expression levels of interleukin-6 (IL-6) and interleukin-10 (IL-10) in colon tissue, and a quantitative analysis was performed; Western blot was used to measure the protein expression levels of nitric oxide synthase (NOS), choline acetyltransferase (ChAT), c-fos, and vasoactive intestinal peptide (VIP) in colon tissue; ELISA was used to measure the expression level of tryptophan hydroxylase 1 (TPH1) in intestinal contents. Results Baitouweng Decoction significantly increased the body weight and colon length of UC rat (P<0.05), upregulated the expression levels of IL-10, ChAT, and VIP (P<0.05), and reduced DAI score and the expression levels of IL-6, NOS, c-fos, and TPH1 (P<0.05). It could also improve the UC-like pathomorphological changes in the intestinal tract of mice. Conclusion Baitouweng Decoction may alleviate intestinal injury in UC rats by regulating the expression of brain-gut peptides and the release of inflammatory factors.