As a special traditional Chinese medicine, Astragalus polysaccharides for injection (APS, batch no. Zhunzi Z20040086) includes complex polysaccharide macromolecules that may increase the risk upon application. Although fingerprints for quality control are available, the specific active ingredients are unclear. Identifying the active components is the key to reduce the risk of adverse reactions of the drug. In this work, APS was mainly separated into two components, namely, macromolecular component (APS-I) and small molecular components (APS-II). The molecular weight measurement revealed that the average molecular weight of APS-I exceeded 500 kDa, and that of APS-II was 10 kDa. Monosaccharide-composition analysis revealed that APS-I consisted of glucose, galactose, arabinose, rhamnose, and galacturonic acid, with a ratio of approximately 1.5:1:5.4:0.08:0.1. Meanwhile, APS-II consisted of glucose, galactose, arabinose, rhamnose, and galacturonic acid, with a molar ratio of 9:1:1.4:0.04:0.001. Methylation, FT-IR, and NMR analysis indicated that the APS-I monosaccharide residue was linked as follows: D-Glcp-(1→, →4)-D-Glcp-(1→, →2)-L-Rhap-(1→, D-Araf-(1→, →5)-D-Araf-(1→, →2,5)-D-Araf-(1→, →4)-D-Galp-(1 → . Meanwhile, the APS-II monosaccharide residue was connected as follows: α-D-Glcp-(1→, →4)-α-D-Glcp-(1→, →6)-α-D-Glcp-(1→, →4,6)-α-D-Glcp-(1→, →3,4,6)-α-D-Glcp-(1→, →2)-α-L-Rhap-(1→, α-D-Araf-(1→, →5)-α-D-Araf-(1→, →4)-β-D-Galp-(1 → . Screening experiments on their in vitro immunological activity showed that APS-II had stronger effect on innate and adaptive immunities than APS-I. In vivo animal experiments showed that APS-II can increase the leukocyte level of cyclophosphamide immunosuppressed mice and improve their immunomodulatory ability. Therefore, APS-II is the main active ingredient of APS and is expected to become a new generation of APS products.