The present invention relates to a virus-resistant pharmaceutical composition, which comprises effective dose of Antrodia extracts. The Antrodia extracts comprise Antrodia fermentation liquid or extracts of Antrodia fruiting body. Antrodia extracts are extracted by organic solvents. The viruses mentioned in present invention are influenza A virus (H1N1 or H3N2), or Enterovirus (EV71).