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Low molecular weight heparins (LMWHs), depolymerized from unfractionated heparin (UFH), are widely used as anticoagulant drugs in clinic. The variable degradation methods result the different types of LMWHs, such as enoxaparin prepared by alkaline degradation following benzylation and nadroparin degraded by nitrous acid and subsequent reduction. They have different anticoagulant activities, molecular weight and special oligosaccharide sequences. Oligosaccharide analysis of the heparinase-catalyzed digestion products of heparin and LMWHs is an important way to explore the fine structural composition. In this work, a MHC-2D-LC-MS system using SAX followed by SEC and tandem to MS was applied to analyze the heparinase-products of LMWHs. 15 components of enoxaparin and 20 components of nadroparin were separated and unambiguously characterized with mass spectrum, including eight common disaccharides, and the special structural domains resistant to enzyme digestion which have the 3- O sulfated residue and/or characteristic terminal residues and the linkage region tetrasaccharides. • The platform of MHC 2D-LC linked to MS was applied to analyze digested LMWHs. • SAX is the first dimensional, SEC is the second dimensional chromatography. • 15 and 20 structural domains in enoxaparin and nadroparin were identified. • Common structural framework and special structural domains were observed. [ABSTRACT FROM AUTHOR]