To address the structure–activity relationship of Chlamys farreri polysaccharides on their immunostimulatory efficacy, two polysaccharides (CFP-1 and CFP-2) were extracted from Chlamys farreri by hot water extraction, and separated through column chromatography. The isolated CFPs were chemically analyzed to clarify their physicochemical characteristics and cultured with murine macrophage RAW264.7 cells, in order to evaluate their immunostimulatory efficacy. Despite the fact that both CFP-1 and CFP-2 were mainly comprised of glucose lacking the triple-helix structure, as revealed through preliminary physicochemical analyses, obvious differences in regard to molecular weight (Mw), glucuronic acid content (GAc) and branching degree (BD) were observed between CFP-1 and CFP-2. In in vitro immunostimulatory assays for macrophage RAW264.7 cells, it was demonstrated that CFP-2 with larger Mw, more GAc and BD could evidently promote phagocytosis and increase the production of NO, IL-6, TNF-α and IL-1β secretion, by activating the expression of iNOS, IL-6, TNF-α and IL-1β genes, respectively. Hence, CFP-2 shows great promise as a potential immunostimulatory agent in the functional foods and nutraceutical industry, while CFP-1, with lower molecular weight, less GAc and BD, displays its weaker immunostimulatory efficacy, based on the indistinctive immunostimulatory parameters of CFP-1.