Abstract: In order to investigate the pharmacologically active components of D. racemosum and D. buxifolium, as well as the material basis for D. buxifolium’s resistance to gall parasitism, this study utilized UHPLC-MS/MS technology to compare the metabolites of the two species. Differential components were identified using multivariate statistical analysis, and the pathways of the differential metabolites were analyzed using HMDB and KEGG databases. The results identified a total of 720 secondary metabolites across 15 categories in D. racemosum and D. buxifolium. Among these, 263 differential metabolites were identified in 13 categories, with lipids and lipid-like molecules (36.22%) and phenylpropanoids and polyketides (31.53%) showing the most significant differences. Key metabolites were identified, including geniposidic acid and succinic acid, which have antidiabetic properties; 3-hydroxymethylbenzoic acid, chlorogenic acid, and traumatic acid, which contribute to lipid reduction; and epicatechin, which has cardioprotective effects and the ability to inhibit liver fibrosis. Furthermore, highly active flavonoids such as kaempferol, quercetin, and salvia emodin, as well as the polyphenol epigallocatechin, were identified, providing valuable insights for the medicinal development of D. racemosum and D. buxifolium. Compared to D. buxifolium, D. racemosum exhibited 93 upregulated and 170 downregulated components. The differential metabolites were primarily enriched in metabolic pathways related to plant hormone biosynthesis and signal transduction, amino acid biosynthesis and metabolism, phenylpropanoid biosynthesis, and aminoacyl-tRNA biosynthesis. Notably, the high levels of jasmonic acid in D. buxifolium may be the key factor explaining its resistance to gall parasitism.