Phyllophorus proteus is a low-value sea cucumber from Indonesia and other tropical peripheral waters. In this study, a fucosylated glycosaminoglycan (FG) was extracted from P. proteus. It consists of GlcA, GalNAc, and Fuc, with a molecular weight of 67.1 kDa. The degraded FG (dFG) was prepared by β-elimination. Structural analysis revealed that the main chain of dFG was composed of GalNAc and GlcA, linked alternately by β1,3 and β1,4 glycosidic bonds. The sulfate group was located at the 4 and 6 positions of GalNAc. Fuc was attached to the 3 position of GlcA by an α1,3 glycosidic bond, and the side chain of Fuc exhibited various sulfate substitutions. FG significantly prolonged the coagulation time of APTT, PT, TT, and FIB, surpassing the effect of LMWH, thereby demonstrating its ability to exert anticoagulant effects in both the endogenous and exogenous coagulation pathways. Conversely, dFG had no significant effect on the clotting time of PT, suggesting its lack of impact on the intrinsic coagulation pathway. This study elucidates the structural properties and potent anticoagulant activities of fucosylated glycosaminoglycan from P. proteus.