A method of analyzing a sugar chain by high performance liquid chromatography uses a column packed with a stationary phase including anion and cation exchangers. A fluorescence-labeled sample is prepared for the analysis by decomposing glycosaminoglycans to be analyzed into their constitutional units being disaccharides, capturing the disaccharides by glycoblotting, releasing the disaccharides by acid treatment, and subsequently reductively aminating the released disaccharides. In this method, two or more types of glycosaminoglycans can be simultaneously analyzed.