This study was aimed to investigate the role of sequence similar matching (SSM) method in prediction of GVHD after HLA unmatched allogeneic hematopoietic stem cell transplantation (allo-HSCT). The data from 23 patients undergoing HLA unmatched allo-HSCT were analyzed and calculated by SSM method. The results showed that the incidence of acute and severe GVHD were significantly less in the allo-HSCT cases with total SSM value less than 55. In conclusion, the SSM method can be used to predict GVHD in the HLA-unmatched allogeneic hematopoietic stem cell transplantation.