A method for incubating fruiting bodies of Antrodia cinnamomea is disclosed. The method comprises steps of: (a) obtaining a hymenium slice from a fruiting body of Antrodia cinnamomea (S1) (b) transferring the hymenium slice to a selective culture medium for incubation to obtain an isolated strain (S2) (c) transferring the isolated strain to a bagasse culture medium for incubation (S3) (d) subjecting proliferation by liquid culture or solid culture to obtain large-scale liquid spawn or solid spawn (S4) (e) inoculating a wood segment with the liquid spawn or the solid spawn and subjecting incubation (S5) and (f) re-inoculating the wood segment with mixed single-spore colonies of Antrodia cinnamomea and subjecting incubation until fruiting bodies are produced (S6).
