To analyze the differences of metabolite in different parts of Paeonia lactiflora Pall., the herbaceous peony cultivar named "Cream Bowl" was selected as material, based on non-targeted metabolomics technology combined with principal component analysis and partial least squares analysis, the metabolites in the flowers, leaves and roots of herbaceous peony were explored. The results showed that 1 654 metabolites were detected, the similarity of metabolite types in the flowers and roots of herbaceous peony is relatively high. There were 511, 476, and 490 differential metabolites were found in flowers vs leaves, flowers vs roots, and leaves vs roots, respectively. These differential metabolites were mainly lipids and lipid molecules, organic acids and their derivatives, as well as phenylpropane and polyketide compounds. The metabolites were mainly distributed in 16 metabolic pathways, and the pathways with the highest enrichment of metabolites are global and overview maps, amino acid metabolism, and biosynthesis of other secondary metabolites. This study analyzed the differential metabolites in different parts of herbaceous peony, as well as provided theoretical basis for the comprehensive utilization of herbaceous peony resources.