Poria cocos F.A.Wolf is a Chinese traditional medicine used to treat chronic gastritis, edema, nephrosis, gastric atony, and acute gastroenteric catarrh. Polysaccharides are the main active component of P. cocos. We obtained polysaccharides PCP-1, PCP-2, and PCP-3 from the degradation of P. cocos polysaccharides (PCP) with different concentrations of H2O2 solution. Molecular weights were determined by high performance size exclusion chromatography. HPLC analysis of monosaccharide composition confirmed that PCP-1, PCP-2, and PCP-3 are heteropolysaccharides composed of glucose and arabinose. IR spectra indicated obvious characteristic peaks of polysaccharides. The antioxidant activities of these polysaccharides were evaluated by established in vitro systems, including scavenging activity of hydroxyl radicals, ABTS radicals, and ferrous ions. The degradation polysaccharides exhibited obvious and concentration-dependent antioxidant properties. In addition, DNA binding analysis showed that PCP-1 had a stronger capacity than other polysaccharides to interact with DNA. However, each polysaccharide had a certain capacity for DNA damage protection.