Central composite design (CCD), together with multiple linear regression, was successfully used to optimize the electrophoretic buffer system of micellar electrokinetic capillary chromatography (MEKC) for the determination of albiflorin, paeoniflorin, liquiritin, and glycyrrhizic acid in the traditional Chinese medicine (TCM) prescription, Yangwei granule. Concentrations of sodium deoxycholate (SDC) and borate, and proportions of ammonia, acetonitrile, and methanol were optimized. The total resolutions of peaks between the analytes and their adjacent peaks in real samples were integrated into the evaluation index of separation efficiency. The optimum electrophoretic buffer contained 80 mmol/L SDC, 20 mmol/L borate, 5% (v/v) methanol, 0.5% (v/v) ammonia, and 5% (v/v) acetonitrile. The correlation coefficients (R(2)) between the peak areas and the corresponding concentrations of analytes were greater than 0.9956. The limits of detection (LODs) (S/N=3) of the analytes were 0.97-4.00 μg/ml. The results indicate the superiority of CCD in optimizing the separation conditions of complex samples such as TCM prescriptions.