Background and purpose: intrinsic Xase (iXase) is the final and rate-limiting enzyme complex in the intrinsic coagulation pathway, which may be the target for anticoagulation and anti-thrombosis with lower bleeding tendency. A depolymerized fucosylated glycosaminoglycan (dHG-5) with molecular weight of 5.2 kDa was prepared from sea cucumber Holothuria fuscopunctata, showed promising druggability as an anticoagulant targeting iXase. Like heparin, the drug candidate dHG-5 is composed of a series of oligosaccharides. Therefore, it is necessary to clarify these oligosaccharides’ structures and contents in dHG-5, and their contribution to the pharmacological activities of dHG-5. Experimental approach: These oligosaccharides’ structures were confirmed by 2D NMR and MS spectra. The coagulation factor inhibition and factor IXa-binding activities were analyzed by chromogenic substrates and BLI, respectively. Anticoagulation was evaluated by clotting time. Antithrombotic activity and bleeding risk were evaluated by deep venous thrombosis model and tail-bleeding model, respectively. Key results: Our data revealed that 1) the nine purified oligosaccharide components were homologous and shared the common formula, which accounted for about 95% of dHG-5, 2) the relationships of anti-iXase, f.IXa-binding, APTT-prolonging and antithrombotic activity potenies (y) and oligosaccharides’ molecular weight (x) fitted well with power function (y = a × x b), 3) the activity potencies of dHG-5 were approximately equivalent to the weighted average sum of those of its oligosaccharides, 4) dHG-5 showed antithrombotic activity with low bleeding tendency and predictable pharmacodynamics characteristic. Conclusion and Implications: dHG-5 has antithrombosis with low bleeding tendency, and clear chemical composition and pharmacological properties, which makes a good preparation for the clinical study.