The two novel polysaccharides, DMP‐1 and DMP‐2, with molecular weights of 4.1553×105 kDa and 1.9764×105 kDa, respectively, were isolated from Dracocephalum moldavica. The structural characterization indicated that DMP‐1 and DMP‐2 shared a similar backbone consisting of →5)‐Araf‐(1→, Manp‐(1→, Glcp‐(1→, →2)‐Manp‐(1→, →6)‐Glcp‐(1→ and →3,6)‐Galp‐(1→ with a different molar ratios and triple‐helix structures with α‐ and β‐type glycosidic bonds. The anti‐complementary activity evaluation showed that DMP‐1 and DMP‐2 had strong complement inhibition through the classical pathway (CP), alternative pathway (AP) and lectin pathway (LP). Mechanistic studies indicated that DMP‐1 can block the activation cascade of the complement system by targeting C2, C3, C5, C9, Factor B and Factor P, and that DMP‐2 inhibited complement activation by blocking C2, C3, C4, C5, C9 and Factor B.