Objective To analyze the clinical efficacy of hematopoietic stem cell transplantation (HSCT) in the treatment of hematological neoplastic diseases in children. Methods The clinical data of 86 children with hematological neoplastic diseases who underwent HSCT in the Affiliated Hospital of Xuzhou Medical University from March 2016 to August 2020 were retrospectively analyzed. Results Eighty-six children (50 boys and 36 girls) with HSCT were included, and the median age was 11 (9-14) years. There were 27 cases of acute lymphoblastic leukemia (ALL), 28 cases of acute myeloid leukemia (AML), 16 cases of aplastic anemia (AA), 5 cases of lymphoma, 4 cases of chronic myeloid leukemia (CML), 3 cases of myelodysplastic syndrome (MDS), 1 case of neuroblastoma (NB), 1 case of systemic neosclerosis (SSC) and 1 case of adrenoleukodystrophy (ALD). There were 7 cases of autologous transplantation, 4 cases of umbilical cord blood transplantation and 75 cases of allogeneic hematopoietic stem cell transplantation (allo-HSCT). The median follow-up time of 86 patients was 29.5 (17.6-44.0) months. A total of 84 patients were successfully implanted, and 1 patient failed autologous transplantation and 1 failed allo-HSCT. Fourteen patients relapsed, including 4 patients with autologous transplantation and 10 patients with allo-HSCT. Six patients developed grade Ⅲ/Ⅳ GVHD, all of whom were allo-HSCT. Twenty patients died, including 4 patients with autologous transplantation and 16 patients with allo-HSCT. Fisher's exact test showed that there was significant difference in the occurrence of grade Ⅰ/ⅡGVHD among the four groups of autologous transplantation, cord blood transplantation, SIB homozygous and half homozygous (P<0.001). Conclusions HSCT is an effective method to treat a variety of malignant diseases in children, but recurrence and severe GVHD after transplantation are important factors affecting the prognosis. Preventing recurrence and controlling rejection are very important in children's HSCT.