Food allergy in children is a major early manifestation of the atopic march. Environmental and dietary factors in early life can be involved in the development of food allergy and its related diseases by affecting the intestinal microecology, altering intestinal barrier function and intestinal immunophenotype. Microecological therapy is expected to prevent and treat food allergy and other allergic diseases to some extent. More studies are still needed to verify the efficacy and safety of certain specific prebiotics and/or probiotic in the prevention and treatment of food allergy.