High molecular weight glutenin subunit (HMW-GS) is important for processing quality of wheat. High performance capillary electrophoresis (HPCE) is increasingly used in the work of separation and identification due to its advantages of small sample, rapidness and high precision. However, this technique has been seldom used in wheat HMW-GS study and its separation system needs improvement in analytical speed and discernibility. On the basis of HMW-GS identification with SDS-PAGE and molecular markers, an high-efficiency separation system of HPCE was set up using Chinese Spring as the standard. The system components (pH 2.5) were 75 mmol L -1 IDA, 0.05% HPMC, and 15% ACN. The electrophoresis parameters were 25 μm of inner diameter of the capillary, 200 nm of detection wavelength, 20 kV of separation voltage, and 30°C of operating temperature. Using mixed injection method, the standard spectrums were obtained for 18 subunits. Their migration order was 1Dy12→ 1Dy10→ 1By9→ 1By8→ 1By18→ 1By16→ 1By20→ 1Bx17→ 1Bx20→ 1Bx13→ 1Bx6→ 1Bx7→ 1Ax2*→ 1Ax1→ 1Dx5→ 1Dx4→ 1Dx3→ 1Dx2, and standard peak time of these subunits was 9.39, 9.69, 10.30, 11.70, 11.89, 12.09, 12.22, 12.36, 12.62, 12.83, 13.08, 13.18, 13.50, 13.73, 14.04, 14.24, 14.46, and 14.73 min, respectively. The relative standard deviation was smaller than 0.2%. The y-type and x-type subunits appeared in the phases of 9.39-12.36 min and 12.36-14.76 min, respectively, between which there was 1Bx17 as the boundary. These results indicate that the HPCE separation system is applicable in rapid identification of HMW-GS in wheat germplasm resources when we simultaneously consider migration order, standard peak time, and HPCE spectrum.