Although Codonopsis pilosula (common name: Dangshen) is a widely used medicinal edible herb, but the structural divergence and functional specificity of polysaccharides from its intraspecific varieties remain understudied. Therefore, this study explores the structural characteristics and immunomodulatory activities of polysaccharides from two varieties of Codonopsis pilosula, namely, Codonopsis pilosula Nannf. var. modesta (Nannf.) L.T.Shen and Codonopsis pilosula (Franch.) Nannf. Crude polysaccharides were extracted via water extraction–ethanol precipitation and purified using DEAE-52 column chromatography to obtain homogeneous fractions WCP (6.444 kDa) and BCP (15.71 kDa). Structural analyses confirmed both to be fructans, but with distinct linkage patterns: WCP contains Fruf-(2→, Glcp-(1→, →1)-Fruf-(2→, →1,6)-Fruf-(2→ linkages, while BCP additionally harbors →6)-Fruf-(2→ linkages. This structural divergence correlates with the observed differences in their physical properties and biological activities. Using zebrafish models, WCP and BCP were found to increase the density of neutrophils and macrophages, while reducing the levels of pro-inflammatory cytokines including IL-1β, IL-6, and TNF-α (p < 0.05 vs. model group). These results support their immunomodulatory potential, providing a scientific basis for developing Codonopsis polysaccharide-based functional food ingredients.