In this study, the digestion and fermentation properties of the bioactive water-soluble polysaccharide (HEP-W), and alkali-soluble polysaccharide (HEP-A) from Hericium erinaceus and the impact on the human colonic microbiota were determined using simulated saliva–gastrointestinal digestion and human fecal fermentation models in vitro. The basic physicochemical properties of HEP-W and HEP-A were determined at the same time. The results showed that the in vitro simulated digestion had almost no effect on the physicochemical properties of HEP-W and HEP-A, indicating that HEP-W and HEP-A were partially degraded. During fermentation, HEP-W and HEP-A increased the relative abundance of the dominant butyric acid-producing genera, the microbial community structure was significantly regulated, the gas production and short-chain fatty acid production in the fermentation broth were significantly increased, and the pH of the fermentation broth was reduced. There were structural and other differences in HEP-W and HEP-A due to different extraction methods, which resulted in different results. These results suggest that HEP-W and HEP-A may be potential gut microbial manipulators to promote gut health by promoting the production of beneficial metabolites by intestinal microorganisms using different butyric acid production pathways.