Flavonoids have antioxidant, anti-inflammatory and immunomodulatory properties, and may alleviate food allergic reactions and intestinal inflammation induced by ω-5 gliadin, a main allergen of wheat food allergy in children. In this study, a human basophil KU812 cell degranulation model and a Caco-2 monolayer cell model were constructed in vitro to evaluate the effects of four flavonoids on the allergenicity of ω-5 gliadin peptides and ω-5 gliadin peptide-induced barrier damage in Caco-2 intestinal epithelial monolayers. The results show that baicalein, luteolin, isorhamnetin and naringenin can significantly inhibit the degranulation of KU812 cells stimulated by ω-5 gliadin-derived peptide P4 and the release of IL-6 and TNF-α. In addition, the four flavonoids significantly inhibited the ω-5 gliadin-derived peptide P4 to induce the release of IL-6, IL-8 in Caco-2 cells, inhibited the release of zonulin, and significantly increase the expression of tight junction proteins Occludin and ZO-1 in the Caco-2 cell monolayer. In conclusion, baicalein, luteolin, isorhamnetin and naringenin inhibit degranulation stimulated by wheat allergen and enhance intestinal barrier functions, which supports the potential pharmaceutical application of the four flavonoids treatment for wheat food allergy.