Nucleosides and polysaccharides are the main bioactive ingredients of Cordyceps genus. Nucleosides shows significant differences in different Cordyceps species. However, the differences of polysaccharides have not been decoded. Here, the structure characters of polysaccharides including molecular weight (Mw) distribution, compositional monosaccharides and glycosidic linkage types were compared in C. sinensis (CS), C. militaris (CM), silkworm-hosted C. militaris (SCM) and Cordyceps fermented products (CSF). Compositional monosaccharides including mannose, glucose and galactose, and 1,4-Glcp glycosidic linkage were found abundant in Cordyceps species. Chemometric analysis showed that Cordyceps exhibit significant differences in structural information especially glycosidic linkage types. Besides, polysaccharides in CS and CSF-4 had obviously strong capacity of stimulating phagocytic, NO production and cytokines secretion. Gray relational analysis and Pearson correlation analysis were performed to further investigate the relationship between key polysaccharide structure and immunomodulatory activities. The results indicated that polysaccharides with relatively large number of 1, 4-Glcp and Mw in range of 7.16 × 10