Myelodysplastic syndrome (MDS) is a group of clonal malignant disorders arise from hematopoietic stem cells. It is mainly manifested by pathological hematopoiesis and high-risk of transforming into acute myeloid leukemia (AML). Allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains the only curable strategy for MDS.The efficacy of allo-HSCT was affected by patient-related factors and treatment-related factors. Recently, investigators have made remarkable progress on the prognosis value of genetic mutations in MDS patients and whether pre-transplant hypomethylating agent (HMA) is necessary. This article focuses on recent advances on the indication and optimal time of allo-HSCT, risk factors affecting allo-HSCT efficacy, prediction and treatment of recurrence after allo-HSCT, in order to provide new ideas for improving the effectiveness of allo-HSCT in treatment of MDS patients.