Bone marrow morphology and karyotyping are effective ways to diagnose myelodysplastic syndromes. However, there are still many patients without these two abnormalities. Recently, there are considerable amount of evidence showing that flow cytometric immunophenotyping is a good approach to detect the abnormal differentiation and maturation of different cell lines and maturation stages of bone marrow cells in MDS patients. The highly reproducible results allow to distinguish MDS from other non-clonal hematocytopenia disorders and have a diagnostic advantage especially in case of low-risk MDS. Meanwhile, it showed a good correlation with the morphology and karyotyping, and with the International Prognostic Scoring System (IPSS) playing a prognostic role. This article reviewed recent advances of research in this field such as the application of FCM in MDS detection, the correlation of FCM parameters with morphologic and cytogenetic diagnosis of MDS as well as the relationship of parameters with typing and prognosis of MDS and so on.