In this report, we present the strategy for the revelation of synergistic effect and elucidation of active fractions from an immunomodulatory complex polysaccharide derived from seven herbs (Lentinula edodes, Ganodorma lucidum, Tremella fuciformis, Chrysanthemum, Lycium barbarum, Codonopsis pilosula and Poria cocos), a formula used as health product in China market, using the combination of HPSEC-MALLS, immunological bioassay and saccharide mapping analysis. The effects of complex polysaccharide and their fractions on RAW 246.7 macrophages demonstrated that the fractions (CD1, CD2, CD3) with molecular weight above 10 kDa exhibited immune activity by directly stimulated NO release and phagocytosis, and induced macrophages to secrete cytokines. Especially, fraction CD2 with molecular weight of 100–1000 kDa showed the strongest bioactivity (EC = 0.19 μg/mL) compared with their individual corresponding herbal polysaccharides fractions due to synergistic effect, which supported the scientific use of Chinese herbal mixture. Moreover, their chemical characters were analyzed by HPSEC-MALLS and saccharide mapping, and the original herbs, including L. edodes, G. lucidum, T. fuciformis and Chrysanthemum, responsible for the immunomodulatory activity were tentatively revealed. Results are beneficial for the quality analysis and formula optimization of complex polysaccharides in both biomedical and functional food field.