Fungal cell wall is composed of various polysaccharides with different structures and diverse bioactivities. Three polysaccharides coded as mycelia hot water-extracted fraction (AC-MHW), mycelia cold alkali-extracted fraction (AC-MCA) and mycelia hot alkali-extracted fraction (AC-MHA) were isolated and purified from the cell wall of Antrodia cinnamomea mycelia with yields of 3.82%, 39.13%, and 10.05%, respectively. The structure analysis showed that all of these polysaccharides were neutral hetero-polysaccharides with a high DB (degree of branching) value and presented as a spherical conformation in NaNO3 solution (0.1 M). Although with different sugar composition and glycosidic bonds, molecular weights of these polysaccharides were all over 107 g/mol. Besides, the results on antioxidant activity and IC50 values indicated that in vitro antioxidant activity of the AC-MCA and AC-MHA were much stronger than AC-MHW, which might be attributed to their greater contents of 1,3-glucosyl residues. It could provide a certain reference for the study and development of Antrodia cinnamomea polysaccharides as ingredients of functional foods.