Three fucosylated chondroitin sulfate (fCS) were obtained from edible sea cucumbers Apostichopus japonicus, Stichopus chloronotus and Acaudina molpadioidea collected from China. fCS from Stichopus chloronotus was firstly reported. The detailed structures of fCSs, particularly the fucose branches, were investigated and compared. 1H and 13C NMR of the polysaccharide identified three sulfation patterns of fucose branches: 4-O-, 2,4-di-O, and 3,4-di-O-sulfation variously existed in different fCSs. The backbone structure was confirmed by the monosaccharide composition and two-dimensional NMR. Antioxidant properties of fCSs were evaluated by the scavenging abilities on 1,1-diphenyl-2-picrylhydrazyl, nitric oxide radicals and inhibition of lipid peroxidation. The results showed that their activities could be affected by the sulfation patterns of the fucose branches, and O-4 sulfation is particularly important for its activities. The anti-inflammatory assays of fCS-Am showed significant reduction of the carrageenan induced edema in a dose depended manner, which could be used as a potential antiallergic agent.