Accumulating data indicate that cancer stem cells play an important role in tumorigenesis and are underlying cause of tumor recurrence and metastasis, specifically in chronic myeloid leukemia (CML). We aim to detect the miRNAs that are correlated with the cancer stem cells in CML to provide theoretical basis for clinical application. We first analyzed microRNA expression profiles of CML leukemia patients compared with normal controls by microarray analysis and validated the results by real-time PCR. A single microRNA signature classified CML from normal was detected. We also determined the absolute copy numbers of these three microRNAs in normal adults. The results showed that three microRNAs (miR-150, miR-23a, and miR-130a) were identified to significantly decrease in expanded 38 CML patients compared with 90 normal controls. Molecular and statistical analysis showed that the decreased microRNAs were significant in clinical analysis. All these results indicated that those three microRNAs could act as a tumor suppressor and their decreased expression might be one of the causes of leukemia. Accordingly, clarifying their regulatory mechanisms might delineate their potentials as drug targets of gene therapy for CML.