Inflammatory bowel disease (IBD) is a comprehensive term for chronic or relapsing inflammatory diseases occurring in the intestinal tract, generally including Crohn’s disease (CD) and ulcerative colitis (UC). Presently, the pathogenesis of IBD is unknown, yet multiple factors have been reported to be related with the development of IBD. Flavonoids are phytochemicals with biological activity, which are ubiquitously distributed in edible plants, such as fruits and vegetables. Recent studies have demonstrated impressively that flavonoids have anti-IBD effects through multiple mechanisms. These include anti-inflammatory and antioxidant actions; the preservation of the epithelial barrier integrity, the intestinal immunomodulatory property, and the shaping microbiota composition and function. In addition, a few studies have shown the impact of flavonoids on enterohormones release; nonetheless, there is hardly any work showing the link between flavonoids, enterohormones release and IBD. So far, the interaction between flavonoids, enterohormones and IBD is elucidated for the first time in this review. Furthermore, the inference can be drawn that flavonoids may protect against IBD through modulating enterohormones, such as glucagon-like peptide 1 (GLP-1), GLP-2, dipeptidyl peptidase-4 inhibitors (DPP-4 inhibitors), ghrelin and cholecystokinin (CCK). In conclusion, this manuscript explores a possible mechanism of flavonoids protecting against IBD.