To elucidate the material basis underlying the formation of superior quality in ancient tea treeplants and evaluate their metabolic differences from cultivated tea treeplants, as well as assess their potential for cultivar development, this study employed one bud and two leaves from ancient tea treeplant cultivars ‘Yaolongshan Jinfenghuang’ (JFH) and ‘Zhulinping’ (ZLP), along with the elite cultivated cultivar ‘Fuding Dabaicha’ (FDDB) as experimental materials. Untargeted comparative metabolomic analysis was conducted using UHPLC-Q-TOF-MS technology. Principal component analysis revealed significant differences in global metabolic profiles between ancient tea treeplants and cultivated varieties. Pathway enrichment analysis indicated that differential metabolites were primarily enriched in key pathways including plant secondary metabolite biosynthesis, phenylpropanoid biosynthesis, flavonoid biosynthesis, and amino acid biosynthesis. Analysis of common differential metabolites demonstrated that phenolic acids and flavonoids such as 4-caffeoylquinic acid, epigallocatechin gallate, and myricetin-3-O-glucoside were significantly upregulated in both ancient tea treeplant cultivars, whereas polypeptides and amino acid derivatives including linoleoyl lysophosphatidylcholine and phenylalanine-glycine-lysine Phe-Gly-Lys were generally downregulated. Analysis of cultivar-specific differential metabolites revealed that JFH specifically accumulated flavonoid compounds including quercetin-3-O-acetylrhamnoside and 5,6,7,4’-tetrahydroxyisoflavone, along with amino acid derivatives such as L-glutamine and L-histidine, were significantly upregulated. In contrast, ZLP specifically accumulated flavonoids including myricetin-3-glucoside as well as phenolic acids such as 4-hydroxybenzoic acid, but exhibited significantly reduced contents of theanine and procyanidin dimers. Ancient tea treeplants exhibited significant differentiation from cultivated varieties in key metabolic processes including phenylpropanoid and flavonoid biosynthesis and nitrogen metabolism, forming a metabolic pattern characterized by active phenolic acid and specific flavonoid metabolism and generally downregulated free polypeptides and membrane lipid metabolites. Furthermore, JFH and ZLP displayed distinct cultivar differentiation characteristics in specific metabolite accumulation, reflecting the rich genetic diversity of ancient tea treeplant germplasm. These results confirm the specific quality chemical basis of ancient tea treeplants from a metabolomic perspective, providing important germplasm resources and theoretical basis for innovating the current bottleneck of tea quality homogenization.