Euscaphis konishii and Euscaphis japonica are shrubs or small trees belonging to the Staphyleaceae family, and are excellent ornamental fruit plants with high ornamental and medicinal value. There are few studies on the cold tolerance of E. konishii and E. japonica, and their metabolic response to cold is not clear. Here, the non-targeted metabolomics (GC‒MS) technique was used to elucidate the response of E. konishii and E. japonica to cold at the metabolic level. Under cold treatment, E. konishii exhibited 10 upregulated and 1 downregulated differentially expressed metabolites (DEMs), whereas 10 upregulated 7 downregulated DEMs were identified in E. japonica. The contents of key metabolites, such as sugars including raffinose and glucose-6-phosphate, amino acids including lysine and methionine 2, unsaturated fatty acids including linoleic acid, and flavonoid compounds including neohesperidin were increased in E. konishii in response to cold. The contents of key metabolites such as sugars including raffinose, trehalose, and fructose-6-phosphate, amino acids including aspartic acid 1 and aspartic acid 2, and organic acids including pyruvate and taurine were increased, and sugars of sedoheptulose, organic acids of α-ketoglutaric acid, flavonoid compounds of hesperidin were decreased in E. japonica in response to cold. DEMs in E. konishii were significantly enriched in “linoleic acid metabolism”, while the DEMs in E. japonica were significantly enriched in “monobactam biosynthesis”, “cysteine and methionine metabolism”, “taurine and hypotaurine metabolism”, “sulfur metabolism” and “ABC transporters”. This research expounds the metabolic differences of E. konishii and E. japonica in response to cold, and provides a foundation for improving their resistance to cold stress.