A simple and rapid capillary electrophoresis method has been developed for the quantitative analysis of three active compounds: (3R)-7,2'-dihydroxy-3',4'-dimethoxy-isoflavan, kaempferol, and quercetin in Ixeridium gracile. The buffer solution used in this method is 20 mmol/L borate at pH 9.5. The effects of pH value, borate concentration, and applied voltage on migration behavior are systematically investigated. Regression equations reveal good linear relationships (correlation coefficients: 0.9986, 0.9997, and 0.9999) between the peak area of each compound and its concentration. The relative standard deviations of the migration time and peak area are less 1.12% and 3.11% (intraday), and 1.43% and 3.52% (interday), respectively, under the optimized separation conditions. The contents of the three flavonoids in I. gracile are successfully determined within 7.8 min, with satisfactory repeatability and recovery.