A capillary electrophoresis method for fine structural analysis of enoxaparin sodium, comprising: digesting an enoxaparin sodium sample exhaustively with a mixture of heparin degrading enzymes; separating oligosaccharides in the digested enoxaparin sodium sample with capillary electrophoresis, wherein the oligosaccharides include disaccharides, trisaccharides, tetrasaccharides and oligosaccharides with 1,6-anhydro structure; wherein separation conditions of capillary electrophoresis are as follows: the fused silica capillary has a total length ranging from 50 to 100 cm and has an inner diameter ranging from 25 to 75 μm; the running buffer is selected from NaH 2 PO 4 -H 3 PO 4, Tris-H 3 PO 4 or LiH 2 PO 4 -H 3 PO 4 in a concentration ranging from 150-300 mM and in a pH ranging from 1.5-4.0; the running buffer contains MgCl 2 or ZnCl 2 in a concentration ranging from 1-5 mM, and PEG having a molecular weight ranging from 5000 to 100000 in a concentration ranging from 0.1%-5.0% (m/v) is added to the running buffer before use; the applied voltage is in the range from -15 to -30 kV; the pressure for hydrodynamic injection is in the range from 1 to 100 mbar, and the injection time is in the range from 1 to 60 s; after the last monosulfated disaccharide ΔIIA passing through the detection window, a pressure of 5-150 mbar is applied to push ΔIVA passing through the detection window for detection; in the process of electrophoresis, the capillary is thermostatted at 10-40 °C, and the UV detection wavelength is in the range from 230 to 235 nm; pairing peaks present in a electropherogram from the capillary electrophoresis to the oligosaccharides in the digested enoxaparin sodium sample according to the linear relationship between electrophoretic mobilities and charge-to-mass ratio of the oligosaccharides; and quantitatively determining the percentage of each oligosaccharide in total oligosaccharides in the digested enoxaparin sodium sample by using a measured normalized chromatographic peak area. digesting an enoxaparin sodium sample exhaustively with a mixture of heparin degrading enzymes; separating oligosaccharides in the digested enoxaparin sodium sample with capillary electrophoresis, wherein the oligosaccharides include disaccharides, trisaccharides, tetrasaccharides and oligosaccharides with 1,6-anhydro structure; wherein separation conditions of capillary electrophoresis are as follows: the fused silica capillary has a total length ranging from 50 to 100 cm and has an inner diameter ranging from 25 to 75 μm; the running buffer is selected from NaH 2 PO 4 -H 3 PO 4, Tris-H 3 PO 4 or LiH 2 PO 4 -H 3 PO 4 in a concentration ranging from 150-300 mM and in a pH ranging from 1.5-4.0; the running buffer contains MgCl 2 or ZnCl 2 in a concentration ranging from 1-5 mM, and PEG having a molecular weight ranging from 5000 to 100000 in a concentration ranging from 0.1%-5.0% (m/v) is added to the running buffer before use; the applied voltage is in the range from -15 to -30 kV; the pressure for hydrodynamic injection is in the range from 1 to 100 mbar, and the injection time is in the range from 1 to 60 s; after the last monosulfated disaccharide ΔIIA passing through the detection window, a pressure of 5-150 mbar is applied to push ΔIVA passing through the detection window for detection; in the process of electrophoresis, the capillary is thermostatted at 10-40 °C, and the UV detection wavelength is in the range from 230 to 235 nm; pairing peaks present in a electropherogram from the capillary electrophoresis to the oligosaccharides in the digested enoxaparin sodium sample according to the linear relationship between electrophoretic mobilities and charge-to-mass ratio of the oligosaccharides; and quantitatively determining the percentage of each oligosaccharide in total oligosaccharides in the digested enoxaparin sodium sample by using a measured normalized chromatographic peak area.