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Emodin and physcion are abundant anthraquinone compounds found in the traditional Chinese medicinal herb Polygonum cuspidatum Sied. et Zucc. In this paper, emodin and physcion were successfully extracted with supercritical CO2 plus ethanol modifier after the extraction conditions were optimized with uniform design-sequential optimization. Results showed that the ethanol modifier concentration was the main factor for the effective extraction of the emodin. The optimal extraction condition was obtained: 20 MPa, 30 degrees C, and 95% ethanol, at which the yields of emodin and physcion were 0.616 and 0.178 g/100 g, respectively. The yield obtained by supercritical fluid extraction (SFE) was a little lower than that obtained by sonication extraction (SE). The crude extract obtained by SFE was further isolated and purified by semipreparative chromatography with the mobile phase composed of methanol-water (90:1, v/v). Emodin and physcion were obtained with purity 98.6 and 99.1%, respectively, when determined by HPLC, and identification was performed by retention time and UV spectra of the standards. The result suggested that SFE is an alternative and promising method for extraction of the two compounds from P. cuspidatum owing to its environment-friendly properties and fewer coextracts.