A capillary electrophoresis method for quantitatively analyzing characteristic oligosaccharide present in enoxaparin sodium is provided in this invention. The method may be used for quantitatively determining the contents of disaccharides, trisaccharides, tetrasaccharides and in particular oligosaccharides having a 1,6-anhydro ring, which are unique compounds for enoxaparin sodium, within an exhaustively digested enoxaparin sodium sample with a mixture of heparinase I, II, and III, so as to quantitatively determine the molar percentage of oligosaccharides having 1,6-anhydro ring in enoxaparin sodium. The method may be used for the pharmaceutical quality control of enoxaparin sodium during the manufacturing process.