It was shown that different extracts had significant differences in the toxicity of Polygonum multiflorum. In this study, the effect of sample preparation on components and liver toxicity of different extracts from P. multiflorum were determined. Hepatoxic components were discovered based on biomembrane extraction. Comparative chemistry and toxicology between ethanol and water extracts were also performed. The results showed that ethanol extract had much stronger hepatotoxicity, the content of emodin-8-O-β-. d-glucopyranoside, physcion-8-O-β-. d-glucopyranoside, emodin and physcion was significantly higher in ethanol extract than in water extract, while the human hepatocytes extraction showed that 2,3,5,4'-tetrahydroxystilbene-2-O-β-. d-glucopyranoside, emodin-8-O-β-. d-glucopyranoside, physcion-8-O-β-. d-glucopyranoside, emodin and physcion had interaction with human hepatocytes. The hepatotoxic effect of these components was investigated on human hepatocytes LO2 cells and emodin-8-O-β-. d-glucopyranoside, physcion-8-O-β-. d-glucopyranoside, emodin and physcion were finally confirmed to be, at least partial, hepatotoxic components. The results showed that sample preparation has significant effect on components in extracts of P. multiflorum especially the components related to hepatotoxicity. Water extract, the conventional administration form of Chinese herbs, is prefer for phytotherapy before well understanding their chemistry and biological activities.