The invention discloses a CRISPR assisted DNA target enrichment method and an application thereof. sgRNA of a CRISPR/Cas9 system is reformed, novel sgRNA having an acquisition sequence at a 3' terminal is developed, the sgRNA and Cas9 protein without nuclease activity form a compound, the compound and target DNA are in target combination, and a formed DNA-dCas9-sgRNA compound can be acquired by magnetic beads of which the surfaces are fixed with single-chain acquired oligonucleotide, so that the target DNA is in target enrichment and separation from a DNA library or a mixture, and the CRISPR assisted DNA target enrichment method is used for sequence analysis of the target DNA. Compared with a target enrichment method based on hybridization, which is universal at present, the method provided by the invention has notable advantages of being high in simplicity, high in specificity, high in sensitivity, high in flux and the like, and can be deeply applied to preparation of reagents for DNAdetection, diagnosis and treatment.