Pathological scars are dermal fibroproliferative disorders due to rapid inflammatory response after dermal injury. The altered metabolites could reflect pathophysiological changes directly. However, it has not cleared how the metabolites change scars. To explore new ideas of pathological scars from the altered metabolites by using ultra-performance liquid chromatography coupled to tandem mass spectrometry and identifying the key genes. Keloid (KS, n = 10), hypertrophic scar (HS, n = 10), and normal skin (NS, n = 10) were collected. Ultra-performance liquid chromatography coupled to tandem mass spectrometry was used to identify and characterize metabolites. Differential metabolites were analyzed by orthogonal partial least square discriminant analysis and Student t test. The key pathways were analyzed via Kyoto Encyclopedia of Genes and Genomes, and the related enzymes were verified by real-time Polymerase Chain Reaction, both in tissues and their dermal fibroblasts. Two hundred fourteen metabolites were detected in total, mostly were fatty acids and amino acids. In the KS and NS groups, 65 different metabolites were screened ( P < 0.05), and the polyunsaturated fatty acids (PUFAs) metabolism and butyric acid in keloid should be concerned. The messenger Ribonucleic Acid expression of fatty acid desaturase 1 and fatty acid desaturase 2, which are the key enzyme of PUFA metabolism, were lower in KS and keloid-derived fibroblasts, P < 0.05. In HS group, 17 metabolites were significantly different and branched chain amino acids degradation was the key pathway. Moreover, branched chain keto acid dehydrogenase E1 subunit alpha was lower expressed in HS and their fibroblasts compared with NS, P < 0.05. Polyunsaturated fatty acids and butyric acid may be associated with the generation of keloids. The pathogenesis of hypertrophic scars may be involved in branched chain amino acids degradation, which is worth paying attention to.