The flower buds of Styphnolobium japonicum (FBSJ), a medicinal and food plant, exhibit broad application prospects and diverse therapeutic effects, including cooling the blood, stopping bleeding, lowering blood sugar, and exerting antioxidant and anti-inflammatory activities. To provide a reference for the identification, resource development, and utilization, a widely targeted metabolomics study was conducted on FBSJ samples from four production regions in China: Shandong (SJsd), Anhui (SJah), Hebei (SJhb), and Henan (SJhn). In this research, the metabolomic analysis provided the possibility of identifying metabolites to differentiate plants from different origin to broaden a limited metabolome coverage and unclear origin-metabolite-efficacy correlations. A UPLC-MS/MS-based metabolomics analysis was selected to investigate the metabolites of FBSJ from different geographic origins, utilizing the MWDB database and the multi-reaction monitoring mode of triple-quadrupole mass spectrometry (TQMS). A total of 1,559 metabolites were identified, of which 294 were annotated as key active ingredients in traditional Chinese medicine (TCM), and 193 as active pharmaceutical components against 11 diseases, including cancer and diabetes. Among the 708 differential metabolites identified across the four different origin groups, 176 were annotated by KEGG and distributed across 87 metabolic pathways. The most significantly altered metabolic pathway was isoflavonoid biosynthesis (p < 0.01), where SJsd samples exhibited an upregulation trend in key differential metabolites compared to the other groups. Among the 193 disease-active metabolites, 13 (e.g., 3'-Methoxydaidzein, Maackiain) were at least twofold more abundant in SJsd compared to any other origin, highlighting their critical role in explaining SJsd's superior pharmacological potential. This study provides a comprehensive molecular-level analysis of FBSJ metabolites, offering useful insights into its pharmacological analysis across different origins. These findings enhance our understanding of FBSJ metabolites annotated as anti-disease-related components in public databases and offer a valuable reference for investigating their potential in human health applications and the development of novel functional foods.

Background/Objectives: Styphnolobium japonicum cv. Jinhuai (SJvJ) represents a medicinal and edible plant whose metabolite composition is strongly shaped by its growing location. Current quality control methods mainly rely on rutin quantification, lacking comprehensive metabolic markers for origin discrimination. Therefore, this study aimed to profile interregional metabolic differences between Guangxi and Sichuan SJvJ flower buds, identify characteristic differential markers, and clarify relevant metabolic pathways, thereby guiding quality control, germplasm evaluation, and functional food development. Methods: Ultra-high performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was employed to identify metabolites. The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Cancer HSP were applied to screen the key active ingredients of traditional Chinese medicine (TCM-KAIs) and disease-related pharmaceutical ingredients (PDRIs). Specifically, we targeted six highly prevalent human diseases and another five disorders based on therapeutic indications documented in the Chinese Pharmacopoeia. Multivariate analyses, such as principal component analysis, hierarchical clustering analysis, and other statistical methods, were applied to investigate differential metabolites. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was utilized for pathway enrichment analysis of marker metabolites. Results: In total, 1550 metabolites were identified across 12 categories, predominantly flavonoids. Additionally, 152 TCM-KAIs and 204 PDRIs against 11 diseases were screened. Multivariate analyses indicated that geographical origin was closely associated with observed metabolic variation among the tested samples: Guangxi samples accumulated higher lipids and nucleotides, whereas Sichuan samples showed higher levels of flavonoids and phenolic acids. Vanilloloside, protocatechuic acid-4-O-glucoside, and gallic acid-4-O-glucoside were identified as key inter-group biomarkers. KEGG enrichment analysis revealed enhanced metabolism of nucleotide/pyrimidine in Guangxi, whereas zeatin biosynthesis was upregulated in Sichuan, consistent with discrepancies in regional climatic patterns. Conclusions: This study established a more comprehensive metabolomic dataset for FBSJvJ. It also clarified the correlations between origin and quality and unraveled the underlying mechanisms. These findings facilitate origin authentication, standardized quality control, and rational exploitation of FBSJvJ as raw materials of functional foods.