Food allergy prevalence has been rising substantially in recent decades, it has became a global public health problem. Multiple studies suggest that changes in the structure and function of the gut microbiota are closely related to the occurrence of food allergy. Gut microbiota can promote the immune tolerance by regulating immune balance and maintaining the intestinal mucosal barrier function. Now, probiotics, as microecological agents, which can regulate the structure of gut microbiota has received extensive concerns for the application in food allergy. The article reviews the relationship between gut microbiota and food allergy in children, in order to provide new strategies for the prevention and treatment of food allergy in children.