Chlorination disinfection byproducts (CDBPs) can exert adverse human health effects. Many toxicology-based studies confirmed the health hazards of CDBPs, but little research has been done on gut microbiome. We explored the effect of CDBPs on intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The results showed that CDBPs slightly inhibited the production of short-chain fatty acids, and the abundance of Actinobacteria decreased in the transverse colon and descending colon. The abundance of Proteobacteria increased in the ascending colon and descending colon, while it decreased in the transverse colon. The abundance of Firmicutes decreased in both the ascending colon and descending colon. In particular, the abundance of Lachnospiraceae members, Bilophila, Oscillospira, Parabacteroides, Desulfovibrio, and Roseburia increased in the ascending colon, while the abundance of Sutterella, Bacteroides, Escherichia, Phascolarctobacterium, Clostridium, Citrobacter, and Klebsiella increased in the descending colon. The Shannon index differed significantly in both the ascending colon and descending colon before and after exposure. Overall, we demonstrate the feasibility of applying the SHIME model to studying the effects of intestinal toxicity on health of chlorinated by-products. The findings of this study improve our understanding of the health impact of CDBPs on the intestinal microbiota and better control of CDBPs in treated water is recommended.