Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal diseases originating from hematopoietic stem cells. Various types of gene mutations have been found in MDS in recent years with the advance in high-throughput sequencing. Among the genes related to transcription factors, the mutation rate of RUNX1 is higher. RUNX1, a member of the core-binding factor family of transcription factors, is a critical regulator of normal hematopoiesis. RUNX1 mutation can lead to the decrease in the activity of transcription and the binding barrier of DNA. Recent studies have shown that RUNX1 mutation is an independent risk factor for the poor prognosis of MDS. Patients with RUNX1 mutation have a higher risk of transformation to leukemia and a shorter overall survival time. This review mainly discusses the mechanisms of pathogenesis, clinical features and the treatment of MDS patients with RUNX1 mutation.