Disclosed is a method for testing fusion gene. The method comprises: aligning pair-end sequencing data to a whole-genome reference sequence to obtain the first PE group data, the first SE group data, and the first unmap group data; aligning the first unmap group data to a transcript reference sequence to obtain the second SE group data and the second unmap group data; aligning the second unmap group data to a transcript reference sequence to obtain the third unmap group data; estimating insertsize to obtain the proportion of the pair-ends sequenced; merging the SE group data; obtaining a primary candidate set and a fusiongene pair candidate set by combining PE data relation; aligning the half-unmap data to the merging gene sequence of the candidate set to obtain a potential region of a gene fusion breakpoint where the half-unmap locates; obtaining useful-unmap data; fusion simulating the fusion-gene pair candidate set to obtain a fusion sequence being used as a reference sequence and being aligned to the useful-unmap data to obtain fusion gene information. The present invention also provides a system for testing the fusion gene in a sample to be tested.
