The invention discloses a method, primer, probe and kit for detecting six unusual fusion types of BCR-ABL fusion genes such as e6a2, e8a2, e19a2, e1a3, e13a3 and e14a3. The method comprises the following steps: performing primary screening on blood samples by adopting two tubes of fluorescent quantitative polymerase chain reaction (PCR), and quantitatively indentifying specific types of the blood samples belonging to the a2 or a3 group through primary screening judgment. Therefore, the screening cost is reduced, and the detection throughput is also improved. According to the detection method, primer, probe and kit, high sensitivity, high specificity and high detection throughput can be realized, and the method is a rapid and accurate type screening and identifying method.