The invention provides anticancer red ginseng and a preparation method and the application thereof. In the anticancer red ginseng, the molar number of rare ginsenosides and sapogenin accounts for morethan 70% of the molar number of total saponin, wherein the molar number of the sapogenin accounts for more than 20% of the molar number of the total saponin; and under the condition of not introducing any foreign substances, three natural traditional Chinese medicine glycosides enzymes in ginseng are activated, and under the action of three synergistic enzymes, different catalytic reactions are controlled to be activated under different conditions, so that original ginseng saponins which are low in activity and hard to absorb, such as Rb, Rc, Rd, Re, Rf, and Rg1, are converted into the rare saponin and sapogenin which are high inactivity. The anticancer red ginseng has the remarkable anticancer effect and the broad prospect in the preparation of anticancer drugs.