Polysaccharides isolated from fungus Cordyceps militaris display multi-biofunctions, such as immunostimulation, down-regulation of hyperlipidemia, and anti-cancer function. The occurrence of obesity and metabolic syndrome is related to the imbalance of gut microbiota. In this study, the effects of C. militaris and its fractions on modifying metabolic syndrome in mice were evaluated. Mice were fed a high-fat/high-sucrose diet (HFSD) for 14 weeks to induce body weight increase and hyperlipidemia symptoms in mice, and then the mice were simultaneously given a HFSD and C. militaris samples for a further 8 weeks. The results indicated that the fruit body, polysaccharides, and cordycepin obtained from C. militaris had different efficacies on regulating metabolic syndrome and gut microbiota in HFSD-treated mice. Polysaccharides derived from C. militaris decreased the levels of blood sugar and serum lipids in mice fed HFSD. In addition, C. militaris-polysaccharide treatment obviously improved intestinal dysbiosis through promoting the population of next generation probiotic Akkermansia muciniphila in the gut of mice fed HFSD. In conclusion, polysaccharides derived from C. militaris have the potential to act as dietary supplements and health food products for modifying the gut microbiota to improve the metabolic syndrome.