Myelodysplastic syndrome (MDS) is a group of blood-related malignancies caused by disorders of hematopoietic stem cells (HSCs). It is mainly characterized by the ineffective hematopoiesis. Many MDS patients will transform into acute myeloid leukemia (AML) with poor prognosis, often due to infection, hemorrhage and death. However, the molecular mechanism underlying the transformation remains unknown. MicroRNAs (miRNAs), a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression, are considered playing an important role in regulating gene translation during development. Aberrant expression of miRNAs plays an important role in the mutation of HSCs and their transformation to MDS stem cells, suggesting an important mechanism of MDS pathogenesis and its transformation to leukemia. So far, few studies have focused on molecular mechanisms of the transformation of MDS to AML. The role of miRNAs in the transformation needs to be fully understood. Here, we reviewed the molecular mechanism of miRNA involvement in the damage of HSCs, the pathogenesis of MDS and its transformation to leukemia. These results will be of theoretical importance for understanding the mechanism underlying the pathogenesis of MDS, and have potential applications in the prevention and treatment of MDS and in preventing its transformation to leukemia.