Objective To explore the clinicopathological features and treatment of intestinal thrombotic microangiopathopathy (iTMA) associated with allogeneic hematopoietic stem cell transplantation (allo-HSCT) in children, and to provide reference for the early diagnosis and treatment of iTMA. Methods The clinical data of 3 children with iTMA after allo-HSCT treatment were retrospectively analyzed. Results All three patients developed gastrointestinal symptoms such as abdominal pain, intractable diarrhea or severe hematochezia 20 to 50 days after allo-HSCT. Gastroscopy showed different degrees of mucosal bleeding. Colonoscopy showed active or old bleeding, brittle mucous membrane and some erosion. Pathological examination revealed different degrees of mucosal lamina propria disappearance, atypical hyperplasia or absence of glands, and microthrombosis. Virus inclusion bodies were seen in 1 child. Combined with clinical symptoms, iTMA was considered in all the children. After the withdrawal of calcineurin inhibitor and symptomatic treatment, the symptoms of 2 children were relieved in about 2 weeks. After 20 days of stopping the use of calcineurin inhibitors and adding mycophenolate combined with methylprednisolone, plasma exchange, and deinoside, the clinical symptoms of one patient gradually improved. Conclusions iTMA is a complication of allo-HSCT in children and may be associated with graft-versus-host disease (GVHD) and cytomegalovirus infection. For children with severe refractory diarrhea after allo-HSCT, the differential diagnosis of iTMA, GVHD and cytomegalovirus infection should be made by gastrointestinal endoscopy and biopsy pathology as soon as possible, so as to help clinical timely modification of treatment strategies.