In the paper, the influences of the concentration of sodium dodecyl sulphate (SDS) and borax (Na2B4O7), pH value and applied voltage on the MECC of water soluble vitamins--VB1, VB2, VB6, VB12 and VC in fused silica capillary were studied. In the system of SDS-Na2B4O7, the retention times of the vitamins mentioned above increase with the increase of concentration of SDS and Na2B4O7. But if SDS concentration is too high the separation will become worse, and if Na2B4O7 concentration is too high the peak will be broad because the increase of retention time will lead to the increase of diffusion of molecules. With the pH increasing, the separation efficiency is always increasing. The change of the applied voltage has little effect on the separation efficiency. However, at higher pH and applied voltage, the high ionic strength and large current will produce more Joule heat and cause higher background noise. The optimum run buffer for this separation contains 18mmol/L Na2B4O7 and 25mmol/L SDS, with pH at 8.5 by adjusted with hydrochloric acid. The separation was completed within 4min at an applied voltage of 14.0kV. The separation efficiencies ranged from 1.1 x 10(5) to 2.4 x 10(5) theoretical plates/meter. The application of this method to drug analysis is demonstrated.