Three water soluble polysaccharides named SUSP-1, SUSP-2 and SUSP-3 from Selaginella uncinata (Desv.) Spring were purified, which contained different contents of galactose, arabinose, mannose, glucose and xylose, and SUSP-3 had large amount of galacturonic acid. Structural identification showed that the backbone structure of SUSP-1 was composed of (1 → 2)-α-D-Manp, (1 → 4)-α-D-Manp and (1 → 4)-β-D-Xylp. The main chains of SUSP-2 were (1 → 3)-α-D-Galp and (1 → 4)-α-D-Glcp, and SUSP-3 had two fragments and the main chains were (1 → 4)-α-D-GalpA and (1 → 4)-β-D-Xylp. Furthermore, their anti-inflammatory activities were evaluated. THP-1 monocytes were induced into macrophages by phorbol 12-myristate 13-acetat (PMA) and then stimulated by lipopolysaccharides (LPS). The data showed that compared with model groups, SUSP-1, SUSP-2 and SUSP-3 significantly inhibited ROS levels, promoted IL-10 expression, suppressed the mRNA levels of IL-6, TNF-α and IL-1β, and effectively blocked LPS binding to CD14 receptor to reduce inflammation. This study provided new data for the development of natural polysaccharides from S. uncinata with anti-inflammatory activities.