The invention provides a site-directed modification method for DNA viral genome, and the problems in the prior art are solved that induction of site-directed mutagenesis of DNA viral genome is difficult, the operation of inserting an exogenous fragment is complex, and recombination rate is lower. The site-directed modification method comprises: transfecting cells by a plasmid carrying a nuclease system, infecting by a virus, after the cells show pathological changes, collecting the cells with pathological changes, performing freeze-thaw or ultrasonic processing, and centrifuging, separating the liquid supernatant to obtain a progeny virus. The site-directed modification method is capable of realizing applications to screening of virus attenuated vaccine strains, construction of viral genetic carriers and an oncolytic virus, research on virus function sequences, and the like; during modification of the viral genome, the method helps to improve mutagenesis efficiency, accurately control DNA virus for genome site-directed mutagenesis and specific gene knockout, simplify operation steps of inserting the DNA virus carrier by an exogenous gene, and improve efficiency that the exogenous gene is integrated to the viral genome, so that the work of screening high-flux recombination viruses is convenient to conduct.