Low molecular weight chondroitin sulfate was first prepared by free radical polymerization with hydrogen peroxide in the presence of copper(Ⅱ) iron. Its characterization and physicochemical properties were investigated by physicochemical methods including chemical composition, elementary analysis, IR and AFM. The result showed that molecular weight of chondroitin sulfate from 56956Da to 6906Da by copper catalytic oxidation. The major ingredient such as hexuronic acid, hexosamine and sulfate radical were no significant difference after degradation. The TG-DSC analysis showed the mechanism of thermal decomposition is similar. The AFM analysis indicated this samples exists in aqueous solution with stranded spiral. Part spiral is breaking during degradation. IR analysis showed that the degradation process may caused β-1,4 glycosidic bond fracture but no effect on β-1,3 glycosidic bond.