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Polygoni Cuspidati Rhizoma et Radix (PCR), the rhizome and root of <i>Polygonum cuspidatum</i> Sieb. et Zucc., has been used as an herbal medicine for a long time. In this study, the ultrafiltration combined with high performance liquid chromatography (UF-HPLC) method was developed to screen tyrosinase (TYR), α-glucosidase (α-GLU), and xanthine oxidase (XOD) inhibitors from PCR. Firstly, the inhibitory activity of 50% methanol PCR extract on TYR, α-GLU, XOD, and acetylcholinesterase (ACHE) was tested. The extract showed a good inhibition on the enzymes, except for ACHE. Therefore, UF-HPLC experiments were carried out to screen TYR, α-GLU, and XOD inhibitors from PCR extract. Seven potential bioactive components were discovered, including methylgallate (<b>1</b>), 1,6-di-O-galloyl-D-glucose (<b>2</b>), polydatin-4′-O-D-glucoside (<b>3</b>), resveratrol-4′-O-D-glucoside (<b>4</b>), polydatin (<b>5</b>), malonyl glucoside resveratrol (<b>6</b>), and resveratrol-5-O-D-glucoside (<b>7</b>). Most of them were found as enzyme inhibitors from PCR for the first time, except polydatin (<b>5</b>), which had been reported as an α-GLUI in PCR in the literature. Finally, molecular docking analysis was applied to validate the interactions of these seven potential active components with the enzymes. Compounds <b>1</b>–<b>7</b> were proven as TYR inhibitors, compounds <b>2</b>, <b>4</b>–<b>7</b> were identified as XOD inhibitors, and compounds <b>4</b>–<b>6</b> were confirmed as α-GLU inhibitors. In short, the current study provides a good reference for the screening of enzyme inhibitors through UF-HPLC, and provides scientific data for future studies of PCR.