Objective To explore the efficacy of hematopoietic stem cell transplantation (HSCT) in the treatment of mucopolysaccharidosis type Ⅱ (MPS Ⅱ) by laboratory metabolic indices. Methods The age of hematopoietic stem cell transplantation, the activity of iduronate- 2 -sulfatase (IDS) in peripheral blood leukocytes, the qualitative and electrophoretic results of urinary glycosaminoglycan (GAG) before and after treatment were retrospectively analyzed among 23 MPS Ⅱ children. Results A total of 23 boys were included, with a median transplant age of 4 . 5 years ( 1 . 75 - 12 years). The IDS activity of 23 children before transplantation was significantly lower than the normal value. One hundred days after transplantation, 90 . 9% ( 20 /22 ) of the children had normal IDS activity. By 2 years after transplantation, 100 % ( 9 /9 ) of the children had normal IDS activity. Two years after transplantation, activity was stable in the normal range. There was no statistical difference in IDS activity values of the MPS Ⅱ patients after transplantation in 2 years (P> 0 . 05 ). The content of urinary GAG decreased in 53 . 3 % ( 8 /15 ) of the patients 100 days after transplantation. By the time of data collection, 75 . 0 % ( 15/20 ) of children had decreased urine GAG content after transplantation compared with that before transplantation, but only 2 cases ( 10 . 0 %, 2 /20 ) of children had completely negative urine GAG after transplantation. Conclusions HSCT can restore IDS activity in peripheral blood leukocytes to normal value in MPS Ⅱ children, but it has limited effect on reducing urinary GAG content. It can reduce urinary GAG content to a certain extent, but most of them do not reach the normal level.