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In order to study the effect of polysaccharides produced by Antrodia cinnamomea in submerged fermentation on the intestinal flora of mice and, more broadly, to develop the potential and application value of A. cinnamomea in the field of functional food, we extracted and characterized intracellular polysaccharides (AIPS) and exopolysaccharides (AEPS) from the submerged cultured mycelia and broth of Antrodia cinnamomea. It was found that AIPS and AEPS were predominantly composed of glucose, galactose and mannose. Their average molecular masses were 3.52 × 106 and 4.16 × 105 Da, respectively. AEPS contained a pyran ring, while AIPS had (–C≡C–H) and (C–O) functional groups. Both AIPS and AEPS had strong digestive resistance as demonstrated by their resistance to α-amylase digestion and simulated gastric digestion. Intragastrically administered AIPS and AEPS significantly increased the relative abundance of some beneficial microorganisms (such as Lactobacillus) in the intestine of mice with lincomycin-caused diarrhea, and significantly reduced the relative abundance of some harmful microorganisms (such as Enterococcus, Staphylococcus, Parasutterella and Shigella) (P < 0.05), AEPS being more significantly better than AIPS. This study can provide a new idea and basis for the development of new multifunctional prebiotics.