Abstract Background Ulcerative colitis (UC) is a Th2 infammatory bowel disease characterized by increased IL-5 and IL-13 expression, eosinophilic/neutrophilic infltration, decreased mucus production, impaired epithelial barrier, and bacterial dysbiosis of the colon. Acetylcholine and nicotine stimulate mucus production and suppress Th2 infammation through nicotinic receptors in lungs but UC is rarely observed in smokers and the mechanism of the protection is unclear. Methods In order to evaluate whether acetylcholine can ameliorate UC-associated pathologies, we employed a mouse model of dextran sodium sulfate (DSS)-induced UC-like conditions, and a group of mice were treated with Pyridostigmine bromide (PB) to increase acetylcholine availability. The efects on colonic tissue morphology, Th2 infammatory factors, MUC2 mucin, and gut microbiota were analyzed. Results DSS challenge damaged the murine colonic architecture, reduced the MUC2 mucin and the tight-junction protein ZO-1. The PB treatment signifcantly attenuated these DSS-induced responses along with the eosinophilic infltration and the pro-Th2 infammatory factors. Moreover, PB inhibited the DSS-induced loss of commensal Clostridia and Flavobacteria, and the gain of pathogenic Erysipelotrichia and Fusobacteria. Conclusions Together, these data suggest that in colons of a murine model, PB promotes MUC2 synthesis, suppresses Th2 infammation and attenuates bacterial dysbiosis therefore, PB has a therapeutic potential in UC.