Aconitum carmichaelii is an industrially cultivated medicinal plant in China and its lateral and mother roots are used in Traditional Chinese Medicine due to the presence of alkaloids. However, the rootlets and aerial parts are discarded after collection of the roots, and the non-toxic polysaccharides in this plant were less concerned than the alkaloids and poisonous features. In this study, five neutral and 14 acidic polysaccharide fractions were systematically isolated from different plant parts of A. carmichaelii, and their structural features and bioactivities were studied and compared. The neutral fraction isolated from the rootlets was different from those isolated from the lateral and mother roots, consisting of less starch and more possible mannans, galactans, and/or xyloglucans, which was similar to those of the aerial parts. Pectic polysaccharides containing homogalacturonan and branched type-I rhamnogalacturonan (RG-I) were present in all plant parts of A. carmichaelii. However, more arabinogalactan (AG)-II side chains in the RG-I backbone were present in the aerial parts, while more arabinans followed by AG-I/II were found in the roots. Various immunomodulatory effects determined by complement fixation activity and anti-inflammatory effects on intestinal epithelial cells IPEC-J2 of all polysaccharide fractions were observed. This study highlighted the diversity of polysaccharides present in A. carmichaelii, especially in the unutilized plant parts, and showed their potential medicinal values. This article is protected by copyright. All rights reserved.