The invention discloses a method for detection of gene fusion. The method includes the following steps that 1, the sequences of to-be-detected gene fragments are provided, and sequence comparison with a reference genome is conducted; 2, the to-be-detected gene fragments which are partially same as the sequence of the reference genome are extracted, and consensus sequence portions are labeled; 3, sequence comparison is conducted again on the to-be-detected gene fragments extracted in the step 2 and the reference genome, and if the obtained consensus sequence is not same as the consensus sequence labeled in the step 2, it is speculated that the to-be-detected gene fragments extracted in the step 2 have a gene fusion phenomenon; 4, the authenticity of gene fusion is verified. At the same time, the method and the device further discloses a device for the detection of gene fusion. By means of the method and the device, the gene fusion sequence (less than 1%) with the extremely low concentration can be accurately detected out, and the method and the device are more sensitive to the gene fusion sequence high in fusion concentration.