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Background The prevalence of food allergy has increased dramatically during the last three decades, but currently there was no effective therapy except avoidance of allergen. This study aimed to investigate the effect of a modified Chinese herbal formula, Formula-3, on mast cell degranulation and the anti-allergic activity in both animal and cell models. Methods With OVA-sensitized food allergic model in Brown–Norway rats, we checked tissue injury in the small intestines by H&E staining. The Th2 cytokine levels and IgE production in serum or supernatant of the intestinal mucosa homogenates were analyzed by ELISA. Meanwhile, rat peritoneal mast cell activation and degranulation were examined by Toluidine Blue Stain and the release of histamine was measured. Furthermore, the regulation of Formula-3 on Ca 2 + mobilization was investigated by probing intracellular Ca 2 + with fluo-4 fluorescence. The direct effect of Formula-3 on mast cell stabilization was also studied in RBL-2H3 cell line. Results In vivo Formula-3 administration significantly reduced tissue damage in the small intestines of rat and suppressed Th2 cytokine secretion and IgE production. We demonstrated that Formula-3 treatment significantly suppressed FceR1-mediated mast cell degranulation no matter in OVA-challenged allergic rats or IgE-sensitized RBL-2H3 cell line. Furthermore, Formula-3 significantly decreased Ca 2 + influx through store-operated calcium channels (SOCs) evoked by dinitrophenyl-BSA or thapsigargin in mast cells. Conclusion Taken together, our data indicate that Formula-3 stabilizes mast cells by suppressing FceR1-induced Ca 2 + mobilization mainly through inhibiting Ca 2 + entry via SOCs, thus exerting a protective effect against OVA-sensitized food allergy.