In order to uncover the differences in metabonomics among the different varieties of Sophora japonica ‘Jinhuai’, the metabolites of four varieties of S. japonica (‘Jinhuai’ from early maturity variety (Jinhuai J3), mid-maturity variety (Jinhuai j2 and Jinhuai J4), and late-maturity variety (Jinhuai J6)) were determined using liquid chromatography and mass spectrometry (LCMS). The results showed that there were 1 135 metabolites in S. japonica ‘Jinhuai’, with 632 being differential metabolites. There are 62 repetitive and differential metabolites in the four different varieties of S. japonica ‘Jinhuai’, which were mainly six kinds of substances i.e. lipids and lipid-like molecules (30% of annotated compounds), organic heterocyclic compounds (23.33% of annotated compounds), organic acids and their derivatives (20% of annotated compounds), organic oxygen-containing compounds (10% of annotated compounds), phenylpropanoids (10% of annotated compounds), and alkaloids and derivatives (6.67% of annotated compounds). Differential metabolites are mainly enriched in phenylalanine, tyrosine and tryptophan biosynthetic pathways; the four kinds of S. japonica ‘Jinhuai’ were rich in rutin and quercitrin. Based on the cluster analysis of flavonoids, Jinhuai J6 and Jinhuai J3 were separate groups, whilst Jinhuai J2 and Jinhuai J4 clustered together as a group. S. japonica ‘Jinhuai’ was rich in metabolites, and the metabolite compositions of early-maturing and mid-maturing varieties were highly similar, whereas, the metabolites of latematuring variety differed significantly from the other two types in metabolite composition, with the different metabolites being mainly concentrated in the biosynthesis pathway of aromatic amino acids. The research results can provide references for the rational development and utilization of S. japonica ‘Jinhuai’ germplasm resources.