Objective　To explore fecal bacteria transplantation for the treatment of severe gastrointestinal disease caused by food allergy. Method　The therapeutic process of fecal bacteria transplantation for treatment of severe food allergy gastrointestinal disease was retrospectively analyzed, and the related literature was reviewed. Results　A 2-year-old boy had onset of intestinal infection and diarrhea was persistent even though he had received adequate anti-infection therapy and supportive treatment. Finally, the patient received the treatment of fecal bacteria transplantation and the symptoms were then improved. No adverse reactions were observed in 2 months of follow-up. In foreign literature, fecal bacteria transplantation in children is mainly applied to clostridium difficile infection (CDI) and inflammatory bowel disease (IBD), with efficiency of 90% - 100% and 55.6% - 100%, respectively. While in the domestic literature, fecal bacteria transplantation in children is mainly used in CDI and antibiotic associated diarrhea, and the effective rate is 100%. No serious adverse reactions were found in all the researches. Conclusion　Fecal transplantation is safe and effective in the treatment of children with severe gastrointestinal disease caused by food allergy, but its application in children is not yet mature and needs more in-depth researches.