pH‐zone‐refining countercurrent chromatography has been well explored for separation of organic acids and bases from natural products. However, it has not been investigated in separation of polyphenol compounds so far. In the present work, pH‐zone‐refining countercurrent chromatography was successfully applied in preparative separation of a polyphenol bioactive component resveratrol along with a hydroxyanthraquinone emodin, from traditional Chinese medicinal herb Polygonum cuspidatum using a self‐made type‐J countercurrent chromatographic apparatus. Resveratrol is a polyphenol component with a wide arrange of bioactivities. A biphasic solvent system composed of n‐hexane/ethyl acetate/ethanol/water (3:5:2:6, v/v) was selected, in which 10 mmol L−1 of trifluoroacetic acid was added in the organic phase as the retainer while 10 mmol L−1 of ammonia was added in the aqueous phase as the eluter. The loading sample could reach 300 mg in a single run, in which 35 mg of resveratrol and 156 mg of emodin could be obtained with a high purity of 96.0 and 93.2%, respectively, as determined by HPLC. Meanwhile, an interesting elution sequence for resveratrol and emodin by pH‐zone‐refining countercurrent chromatography was found and discussed compared with conventional countercurrent chromatography. The results showed that pH‐zone‐refining countercurrent chromatography could be used in preparative separation of polyphenol component. An efficient alternative method for preparative separation of resveratrol from Polygonum cuspidatum was established.