Abstract Astragalus polysaccharides (APS) have a wide range of biological activities. Most researchers discuss total APS as the main research object. However, because the relative molecular weight of APS has a wide distribution, in-depth studies on the mechanisms of the biological activity of notable molecules are limited. For example, the relationship between the immunomodulatory effect of APS and its relative molecular weight has not been clearly defined. Therefore, in this paper, we separated and obtained APS of different molecular weights by ultrafiltration technology and then constructed a mouse cyclophosphamide-induced immunosuppression model to investigate the immune activity of APS of different molecular weights. The immune enhancement mechanism of APS was explored by examining changes in routine blood indicators, body weight, immune organs, and differential metabolites in mouse serum. Results showed that APS-I (molecular weight, >2,000 kDa), APS-II (molecular weight, 1.02 × 10^4 Da) and APS-III (molecular weight, 286 Da) could increase the number of immune cells in mouse serum and improve immune organ damage to varying degrees. Among the samples obtained, APS-II showed the best effects. Compared with those in the blank group, 29 metabolites determined by UHPLC Q-Exactive MS in the serum of the model group changed remarkably, and APS-I, APS-II, and APS-III respectively restored 13, 25, and 19 of these metabolites to normal levels. Metabolomics analysis revealed that APS-II is mainly responsible for the immunomodulatory activity of APS. Metabolomics analysis revealed that the mechanisms of this specific molecule may involve the regulation of phenylalanine metabolism, cysteine and methionine metabolism, tricarboxylic acid cycle (TCA cycle) and arginine and proline metabolism. Keywords: Astragalus polysaccharides, structural analysis, metabolomics, serum, immunomodulation, differential metabolites Introduction Astragali Radix (AR) refers to the dried root of the perennial legume Astragalus mongholicus Bunge, which is a traditional Chinese medicine. It is listed as an upper-grade material in Shen Nong’s Herbal Classic and has been used as an immunomodulator in traditional Chinese medicine prescriptions for over 2,000 years. AR has a wide range of uses; for example, it can invigorate the qi, solidify surfaces, reduce water retention and swelling, and support sore muscles. The Ministry of Commerce of China has listed AR as among the country’s 60 strategic key Chinese medicinal materials and 18 main Chinese medicinal materials. In addition, in 2018, AR was included in the Chinese medicine and food homology list. Modern phytochemical and pharmacological experiments have shown that polysaccharides have very strong immunomodulatory activity and are highly abundant in AR ([38]Wu X. et al., 2011). Complex polysaccharide mixtures may be obtained by water extraction and alcohol precipitation from AR. Astragalus polysaccharides (APS) are composed of polysaccharides with diverse structures and different molecular weights distributed over a wide range (5.6 × 10^3–4.8 × 10^6 Da) ([39]Jin et al., 2014). The molecules of APS are mainly composed of different types of functional groups, including dextrans and arabinogalactans. Research on the activity of APS often describes their ability to regulate non-specific immunomodulation, enhancement of specific and non-specific immunity. APS are known to have a variety of biological activities, such as antitumor, antidiabetic, antiviral, cardiovascular, and neuroprotective effects. Studies have shown that these pharmacological activities generally involve immunomodulation ([40]Morten et al., 2008; [41]Jiang et al., 2013; [42]Li et al., 2017). Unfortunately, most available studies focus on total APS or a certain component of APS ([43]Table 1). At present, reports on the separation of total APS according to molecular weight and the structural analysis and immunological screening of the resulting components are scarce. Therefore, clarifying the relationship between the molecular weight, structure and activity of different APS components is necessary to elucidate the medicinal material basis of AR. TABLE 1. Structure characterization of Astragalus polysaccharides (APS). No. Name Molecular weight Main structure Bioactivity References