The symptoms of food allergy present nonspecifically, with 60% of children showing digestive system symptoms such as rectal bleeding, diarrhea, constipation, etc. Clinically, it is highly prone to misdiagnosis and missed diagnosis, leading to over-treatment and delayed treatment, exacerbating the condition and affecting the growth and development of affected children. Three criteria should be followed in the diagnosis of food allergies and associated digestive disorders: (1) clinical symptoms; (2) laboratory testing (oral food challenge) to determine allergens; and (3) a direct correlation between food and symptoms. Rectal bleeding is more common in food protein-induced proctocolitis, and in the neonatal period, it needs to be differentiated from infectious diarrhea and necrotizing enterocolitis. In infancy, it needs to be differentiated from anal fissures, intestinal polyps, intussusception, Meckel’s diverticulum, intestinal vascular malformations, very early-onset inflammatory bowel disease and congenital immunodeficiency disease-related diarrhea. Diarrhea is common in food protein-induced enteropathy and food protein-induced enterocolitis syndrome and needs to be differentiated from lactose intolerance, celiac disease, and diarrhea caused by other reasons. Whether food allergy can cause constipation is still debated, and it needs to be differentiated from congenital megacolon and functional constipation.