Cordyceps guangdongensis, a novel edible mushroom in China, has shown many positive health effects. In this study, we extracted the C. guangdongensis polysaccharides (CGP) from the fruiting bodies, and investigated the mechanism for CGP improved high-fat diet-induced (HFDI) metabolic diseases. We found that CGP notably reduced fat mass, improved blood lipid levels and hepatic damage, and restored the gut microbiota dysbiosis induced by high-fat diet (HFD). Metabolome analyses showed that CGP changed the composition of bile acids, and regulated HFDI metabolic disorder in hepatic tissue. Transcriptome comparison showed that the improvement of hepatic steatosis for CGP was mainly related to lipid and carbohydrate metabolism. Association analysis result revealed that Odoribacter, Bifidobacterium and Bi. pseudolongum were negatively correlated to fat and blood lipid indicators, and were significantly associated with genes and metabolites related to carbohydrate and lipid metabolism. Collectively, these results indicate that CGP may be a promising supplement for the treatment of obesity and related metabolic diseases.