Objective To study and compare the differences of characteristic chromatograms regarding 3 parts from root of Paeonia lactiflora Pall.. Methods Establishment of characteristic chromatogram by high performance liquid chromatography (HPLC). ODS column was used in this study, the column temperature was 30 ℃. The gradient elution of acetonitrile -0.1 % phosphoric acid solution was conducted with the flow rate of 1.0 mL·min-1, and the detection wavelength was 230 nm. Results The characteristic chromatogram showed that 15 common peaks were isolated from cork, 13 common peaks isolated from phloem, 7 common peaks isolated from xylem by analyzing within 3 groups. The characteristic peaks of each part are easy to identify and have good resolution. Principal component analysis obtained three main components in common: paeoniflorin, albiflorin and benzoic acid. There was no significant difference in the content of paeoniflorin in the three parts, and the content of albiflorin in the cork and phloem was not significantly different than that in the xylem, the content of benzoic acid in the cork is higher than that in the phloem. Conclusion Cork contains more components with higher content, xylem has the least components and lower content, phloem is somewhere in between.