Extraction processes significantly alter the structural and functional properties of polysaccharides. In this study, we extracted polysaccharides from Chroogomphis rutilus fruiting bodies (designated as CRP) using four methods, including hot water, ultrasound, microwave and sequential ultrasound-microwave, and designated these polysaccharides as CRP-H, CRP-M, CRP-U and CRP-UM, respectively. All CRPs were heteropolysaccharides with semblable monosaccharide types of glucose, mannose and galactose, mainly constituted of α-d-glucopyranosyl-(1 → 4). The extraction processes significantly affected the molecular weights, monosaccharide proportions, glycosidic bond ratios, branching degrees, triple-helix conformation and surface morphology of the CRPs. Among them, CRP-UM showed the highest yield and most potent antioxidative capacity in vitro and in HL-7702 cells, but the weakest activation of immunostimulatory response in RAW264.7 cells. In contrast, CRP-H exhibited the lowest yield but strongest immunostimulatory activity. Overall, microwave extraction could be utilized as a general and practical CRP extraction approach, based on its relatively high yield and bioactivities.