Two homogenous polysaccharides extracted from Atractylodes macrocephala Koidz. were investigated by water extraction (AMP-FW) and alkali solution extraction (AMP-FA) after purification by anion exchange column and size exclusion chromatography. The molecular weight of AMP-FW and AMP-FA were 2874 Da and 3438 Da, respectively, estimated by high performance gel permeation chromatography (HPGPC). The monosaccharide compositions of AMP-FW and AMP-FA were glucose and fructose at a molar ratio of 0.11:0.89 determined by high performance anion exchange chromatography (HPAEC). The functional groups, glycosidic linkages and the chemical structure were characterized by FT-IR, GC–MS and NMR, which comprehensively indicated a similar inulin-type fructan structure of the two polysaccharides from A. macrocephala. However, the scanning electron microscopy (SEM) results showed different microstructures that irregular lamellar shape for the AMP-FW and spheroid shape for the AMP-FA. The further studies on immunomodulation showed that AMP-FW at 50 μg/mL could significantly (P < 0.05) stimulate RAW 264.7 cells by enhancing the mRNA expression of TNF-α and IL-1β, which had a relative high immunomodulatory potential when compared to AMP-FA. Their activation on different toll-like receptors (TLR) also indicated their different roles in the immunoregulation. Overall, these findings reported here will serve as the basis for further structure-activity relationship studies.