SF3B1 gene mutations are the most frequent mutations found in myelodysplastic syndromes (MDS), and the prognostic implication of these mutations remains controversial. We conducted a meta-analysis of studies assessing the prognostic impact and clinical feature of SF3B1 mutations in MDS patients. The overall hazard ratio for overall survival (OS) was 0.90 (95% confidence interval 0.60-1.35, P = 0.61) in MDS patients with SF3B1 mutations compared to those without. Lower leukemia-free survival was associated with SF3B1 mutations. Subgroup analyses showed that Asian cohorts and Illumina HiSeq 2000 methods were significantly associated with OS. Furthermore, SF3B1 mutations were significantly correlated with a lower level of blast cells and a high level of platelet counts and bone marrow ring sideroblasts. Thus, the current meta-analysis suggests that SF3B1 mutations have no significant impact on the OS of MDS patients, and the hematologic parameters of SF3B1 mutations identify a distinct subset of MDS patients with homogeneous features.