The invention discloses an antiviral complex traditional Chinese medicine and a preparation method and application of the antiviral complex traditional Chinese medicine. The complex traditional Chinese medicine comprises isatis root, rheum officinale, astragalus mongholicus, folium isatidis, houttuynia cordata and polygonum cuspidatum. The antiviral complex traditional Chinese medicine and the preparation method provided by the invention are reasonable in prescription, and simple in preparation technology; as the clinical test shown, the traditional complex traditional Chinese medicine can be applied to preparing medicine for treating or preventing white spot syndrome of cray, hemorragic disease of grass carp, haematopoietic necrosis of crucian, koi herpes virus disease, channel catfish virus disease, iridovirus disease of siniperca chuatsi, and virosis of aquatic livestock; and the antiviral complex traditional Chinese medicine has high efficiency, is safe and has no toxic and side effect, and has a wide clinical application prospect.