Ion mobility-mass spectrometry (IM-MS) was applied to analyses of isomeric oligosaccharides linked by α1-4, α1-6, β1-3, and β1-4 glycosyl linkages. Negative-ion electrospray ionization (ESI) quadrupole IM time-of-flight mass spectrometry allowed the combination of IM separation and collision-induced dissociation (CID) MS/MS product ion analysis. Multimer formations of hexa-saccharide linkage isomers differ from each other, and their molecular shapes were analyzed by ion mobility spectrometry (IMS). The product ion spectra of the oligosaccharide isomers were measured by negative-ion CID-MS/MS for each IM separated peak. The spectrum for each isomer was distinct, and their corresponding linkage structures were identified by MS/MS analysis.