Abstract: To separate and purify fucoidan from Laminaria Japonica by anion-exchange chromatography. To obtain and analyze low molecular weight fucoidan by copper-hydrogen peroxide free radical degradation, High sulfate and fucose content fucoidan were obtained by certain concentration of sodium chloride from anion-exchange column. Infrared spectrum method determined the position of the sulfated group was on C2 or C3.NMR further demonstrated the existence of α-D-pyranose. The molecular weight of fucoidan and low molecular weight fucoidan fractions were analyzed with PAGE electrophoresis. Result revealed that the content of sulfate group and fucose played an important role on the free radical degradation of fucoidan. The fucoidan fraction with high sulfate and fucose content was more difficult to be degraded. The optimal degradation conditions were obtained:500μL 20mg/mL fucoidan solution, with 0.0267mol/L cupric acetate, 10μL 15% H2O2 for F3, F4 and 50μL 15% H2O2 for F6, reacted for 4h at 60℃. Using the method of PAGE could analyze the distribution of the molecular weight of oxidative degradation products.