Complement-mediated inflammation and tissue damage is an important drive to pathology in autoimmune diseases, targeting inhibit the complement activation is promising treatment strategy for these diseases. We performed anticomplement activity-guided fractionation of the water extract of Eclipta prostrata by ion-exchange and size-exclusion chromatography, yielding two bioactive polysaccharides EAP20-1 and EAP20-2. The molecular weights of EAP20-1 and EAP20-2 were respectively calculated to be 5.2 kDa and 6.3 kDa by HPGPC, both polysaccharides was composed by D-Gal, L-Glc, and Ara at different ratios of 7.3:2.7:1 and 7.6:3.1:1. In addition, the main linkage types of EAP20-1 and EAP20-2 were beta-1,4-Gal, beta-1,6-Gal and alpha-1,4,6-Glc according to methylation analyses. EAP20-1 and EAP20-2 exhibited significant inhibitory effect on the complement activation through both classical and alternative pathways and with no influence on the coagulation system. Preliminary mechanism study indicated that both EAP20-1 and EAP20-2 inhibited the activation of the complement system by interacting with C1q, C1r, C1s, C2, C4, C5, C7, and C9 components. (C) 2017 Elsevier Inc. All rights reserved.