Types of BCR-ABL fusion transcripts of chronic myeloid leukemia (CML) are diverse. Different BCR-ABL fusion transcripts express different fusion proteins, and these patients′ incidence, clinical and hematological characteristics and clinical outcomes are not uniform. BCR-ABL fusion transcripts of CML patients can help diagnosing, guiding choices of tyrosine kinase inhibitor (TKI) and treatment monitoring. In order to clarify the clinical significance of different BCR-ABL fusion transcripts in CML, this article reviews the clinical features and prognosis of CML patients with different BCR-ABL fusion transcript types.