The invention relates to a ganoderan complex for treating the hand-foot-and-mouth disease and a preparation method of the ganoderan complex and belongs to the technical field of medicinal health-care food. The ganoderan complex is prepared from components in parts by weight as follows: 20-30 parts of ganoderan, 3-5 parts of a heartleaf houttuynia herb, weeping forsythiae capsule and common anemarrhena rhizome composite traditional Chinese medicine extract, 5-10 parts of saccharose, 0.03-0.05 parts of aspartame, 0.03-0.08 parts of essence and 200-300 parts of pure water. Fat-soluble impurities in lucid ganoderma are removed through ethanol reflux, then the lucid ganoderma is extracted with hot water, precipitated through ethanol and subjected to column chromatographic purification, ganoderan is obtained and compounded with the prepared heartleaf houttuynia herb, weeping forsythiae capsule and common anemarrhena rhizome composite traditional Chinese medicine extract, and the genoderan complex is prepared. Tests indicate that the complex has a remarkable inhibition effect on human enterovirus 71.