Myelodysplastic syndrome (MDS) are a group of progressive, clonal, neoplastic bone marrow disorders characterized by hematopoietic stem cell dysregulation and abnormalities in the immune system. Mesenchymal stem cells (MSC) have gained further interests after the demonstration of an immunoregulatory role. Nevertheless, the immunoregulatory function of MDS bone marrow derived MSC (MDS-MSC) remains poorly defined. In addition, it is not clear whether there are differences in the regulatory functions between low-risk and high-risk MDS-MSC. In this study, we obtain and expand MSC from bone marrow of patients with MDS. Our results show that there are significant differences in the immunoregulatory functions between low-risk and high-risk MDS-MSC. Compare to low-risk MDS-MSC, high-risk MDS-MSC is associated with the presence of increased TGF-β1, higher apoptosis, higher immunosuppressive rate and a poor ability of hematopoietic support. In addition, our results find that there are great differences in the CD4+CD25+Foxp3+Tregs inducible rate between high-risk MDS-MSC and low-risk MDS-MSC. Compared to high-risk MDS-MSC, the inducible rate of CD4+CD25+Foxp3+Tregs of low-risk MDS-MSC is lower. At last, we find that MDS-MSC derived TGF-β1 is largely responsible for the increase in CD4+CD25+Foxp3+Tregs based on knockdown studies. These results elucidate the different immunoregulatory role of MSC in low-risk and high-risk MDS, which may be important for understand the pathogenesis of MDS and the development of novel immunomodulatory strategies for the treatment of MDS.