The invention discloses a method for breeding transgenic plants with the high antiviral property and the application of the method. The inventive method comprises the following steps of: a. checking the frequency of codon usage in a host and determining the rare codons in the host, modifying the codons in a target gene so that some codons in the target gene are mutated into the rare synonymous codons in the host plant; b. constructing a vector containing the target gene with the codon modifications, to be used for transforming plants; c. transforming the plants with the above recombinant vector to obtain the regenerative transgenic plants; d. detecting the transformed plants, screening the transgenic plants in which gene silencing occurs in the target gene, and thereby obtaining the transgenic plants with the high antiviral property. The invention method can be used in breeding highly efficient and stable antiviral transgenic plants.