Objective To observe the efficacy and prognosis of hematopoietic stem cell transplantation (HSCT) in the treatment of inherited bone marrow failure syndromes (IBMFs) in children. Methods The clinical data of children with IBMFs who underwent HSCT in the First Affiliated Hospital of Zhengzhou University from January 2019 to November 2023 were collected, and their clinical characteristics, transplantation preconditioning regimen, hematopoietic reconstruction, and prognosis were analyzed. Results A total of 18 children with IBMFs were enrolled, including 7 cases of Fanconi anemia (FA), 5 cases of dyskeratosis congenita (DKC), 3 cases of Diamond-Blackfan anemia (DBA), 2 cases of congenital amegakaryocytic thrombocytopenia (CAMT) and 1 case of severe congenital neutropenia (SCN). There were 10 boys and 8 girls, with a median age of 8.2 (1.2-14.0) years. The median time of neutrophil engraftment was 11 (9-21) days, and the median time of platelet engraftment was 13 (10-30) days. During the median follow-up of 10.6 （1.0-62.9） months, the bone marrow of 18 patients was completely chimeric. A total of 8 patients developed acute graft-versus-host disease (GVHD), including 2 cases of grade Ⅳ, 2 cases of grade Ⅲ, 1 case of grade Ⅱ, and 3 cases of grade Ⅰ. Two children suffered from mild chronic GVHD. Fifteen patients survived and 3 died. Two children with FA developed transplant-related thrombotic microangiopathy, and they were treated with plasma exchange or defibrotide with poor results, and all died of multiple organ failure. One CAMT patient developed a severe pulmonary infection 28 days after transplantation, and his condition progressed rapidly, ultimately leading to respiratory failure. Conclusions HSCT is an effective method for the treatment of IBMFs in children. According to the different diseases of children with IBMFS, the appropriate preconditioning regimen can be selected to obtain a better curative effect and prognosis.