Aqueous purified extract (PE) was isolated from the crude extract (CE) of the marine mollusk, Ruditapes philippinarum. Two water-soluble polysaccharides, PEF1 and PEF2, were purified from PE. The chemical structures were determined using FTIR, GC, HPLC and 13C NMR. The results indicated that PEF1 and PEF2 were homoglucan–protein complexes with a protein content of 26.0 and 8.2%, and their average molecular weights were about 2.0 × 106 and 5.0 × 103, respectively. The glucan moiety of PEF1 was mainly a (1 → 6)-branched (1 → 4)-α-d-glucan, while that of PEF2 contained (1 → 4)-α-d-glucan and (1 → 6)-β-d-glucan. PE fractions contained large quantities of glutamic acid and aspartic acid, but no cysteine. The antitumor activities were tested both in vitro and in vivo. PE showed significantly the highest tumoricidal activity against human hepatoma SMMC-7721 cells, and PEF1 had better cytotoxicity than PEF2. There was no observed cytotoxicity in human hepatocyte HL-7702 cells within the experimental concentration range for all PE fractions. PE showed antitumor activity against solid tumor Sarcoma 180 in a dose-dependent manner. It also demonstrated stimulating effect on murine lymphocyte proliferation induced by concanavalin A. The results demonstrated that the presence of bound protein, compositional glucan and moderate molecular mass would be helpful to the enhancement of antitumor activities. This study suggested that the polysaccharides isolated from the marine mollusk had a potential application as natural antitumor and immunomodulator agents.