Sevag, trichloroacetic acid and combining Sevag and TCA were used to remove protein from Fucoidan. And the conditions of deproteinization and undeproteinization were discussed to find the influence on the decoloration in Fucoidan. The results showed that methods of combining Sevag and TCA were better than others. By handling Sevag twice, using 1.3 mL TCA every 10 mL polysaccharose solution, the deproteinization rate reached 78.68%, and the polysaccharose loss rate was 28.89%. The decolourization ratio of stock solution was 29.13%, meanwhile, that ratio of deproteinization solution highly was 85.17%.