The present invention relates to a composition comprising probiotics and a polypeptide having binding affinity for IgE as effective ingredients. Particularly, when probiotics and a recombinant protein comprising an extracellular domain of the alpha subunit of IgE Fc receptor were administered in combination, a synergic effect of remarkably reducing food allergy was observed. Therefore, the composition can provide a remarkable therapeutic effect on IgE-mediated allergy disorder, compared to conventional pharmaceutical composition, and thus is expected to find high industrial applicability.