The application discloses a virus integrated DNA enrichment method, a sequencing data analyzing method and a device. The enrichment method of the application comprises the steps of primer hybridizing and extending, magnetic bead separating and washing. The sequencing data analyzing method disclosed by the application comprises the steps of data filtering, splicing and assembling, comparing and breakpoint judging and gene noting. According to the enrichment method disclosed by the application, specific primers are adopted for extending virus genome target genes so as to replace a long probe, so that the cost is low, the efficiency is high, the specificity is high, and the enrichment time is shortened. Compared with a complete genome, the sequencing data analyzing method disclosed by the application can save data amount, can obtain higher sequencing depth, can obtain more virus DNA breakpoint information and integration position information on the host genome, and can obtain clonal integration events supported by more reads, and besides, can detect non-clonal integration supported by single reads, so as to construct a comprehensive prospect integrated on the host genome.