A new assay is developed by use of micellar electrokinetic capillary chromatography to determine stilbene glycoside, emodin and chrysophanol in radix polygoni muliflori. The factors affecting separation are optimized. The running buffer contains 25mmol/L borax, 40mmol/L sodium dodecyl sulfate and 10% ethanol, and its pH value is adjusted to 9.5. Under the optimum conditions, the linear dynamic range is 2.0~1000mg/L for stilbene glycoside, 5.2~260mg/L for emodin and 4.5~225mg/L for chrysophanol. The limits of detection are 1.10,0.29and 0.43mg/L for stilbene glycoside, emodin and chrysophanol, respectively. The average recoveries are 98.8%, 98.8% and 100.7% for stilbene glycoside, emodin and chrysophanol. The assay meets the determination requirement of stilbene glycoside, emodin and chrysophanol in radix polygoni muliflori, and can be applied to quality control of the raw material of radix polygoni muliflori.