A neutral polysaccharide (ALP-1) and an acidic polysaccharide (ALP-3) were purified from Atractylodes lancea (Thunb.) DC. ALP-1 exhibited a linear backbone composed of (2 → 1)-linked β-d-fructofuranose. The backbone of ALP-3 was elucidated as →4)-GalAp-(1 → 3,4)-Rhap-(1→, and with branch chain substituted at O-3 position of →3,4)-Rhap-(1→. The branch chain consists of →3,5)-Araf-(1→, →5)-Araf-(1→, and Araf-(1→. Particularly, ALP-3 could significantly stimulate macrophage proliferation in a dose-dependent manner, and stimulate phagocytic, NO and cytokines production than ALP-1 on RAW264.7 cells. Besides, both ALP-1 and ALP-3 could activate T-cells in Peyer's patch cells and enhance the production of colony stimulation factors. While the ALP-3 also showed better intestinal immune system modulating activity than ALP-1. The result of this study indicated that the structure diversity of polysaccharide is crucial for its bioactivity. And also provided evidence for that carbohydrate polymers in A. lancea definitely contributed to its pharmaceutical effects.