An MEKC method was developed for the determination of the five pharmaceutically important anthraquinones: chrysophanol (1), physcion (2), emodin (3), aloe-emodinin (4), and rhein (5) in Cassia obtusifolia (Leguminosae). A buffer solution (pH 9.00) composed of 20 mM sodium borate, 20 mM sodium deoxycholate (DOC), and 15% ACN was found to be the most suitable electrolyte for this separation. Regression equations revealed linear relationships (correlation coefficients: 0.9993, 0.9992, 0.9996, 0.9989, and 0.9991) between the peak area of each compound (1, 2, 3, 4, and 5) and its concentration. The RSDs of migration times and peak areas were <1.23 and 2.72% within 1 day, respectively. The effects of pH value, surfactant (DOC) concentration, and organic modifier on the migration were also studied. By this way, the contents of five anthraquinones in the extracts of the seed of C. obtusifolia (Leguminosae) from different sources were successfully determined within 14 min.