Fructo-oligosaccharide (FOS) is a typical prebiotic with intestinal health-promoting effects. Here, we explored the anticolitis activity of FOS and clarified the underlying mechanisms. Dextran sulfate sodium (DSS)-induced mice were gavaged with FOS (400 mg/kg) for 37 days, and administration of FOS alleviated DSS-induced colitis symptoms. Besides, FOS improved gut microbiota dysbiosis and modulated the intestinal microbiota-controlled tryptophan metabolic pathways. Targeted metabolomic results showed that FOS significantly increased the colonic levels of indole-3-acetic acid (IAA) and indole-3-propionic acid (IPA) and subsequently increased the expressions of aromatic hydrocarbon receptors (AhR) in the colon and further promoted the expressions of interleukin-22 (IL-22) and intestinal tight junction proteins in the colitis mice. These findings for the first time highlight a novel anticolitis mechanism of FOS by alleviating intestinal microbiota dysbiosis and modulating microbial tryptophan metabolism to promote IAA and IPA production for triggering AhR/IL-22 axis activation.