Abstract: Objective This study aimed to investigate the metabolome differences and medicinal component characteristics of Fortunella hindsii Swingle fruits from two production areas in Fujian Province based on widely targeted metabolomics， so as to provide a scientific basis for regional germplasm conservation，quality certification， functional pro-duct development， and high-value utilization of waste.Method Fortunella hindsii Swingle fruits from two main production areas in Fujian Province—Yongchun County in Quanzhou City， and Songxi County in Nanping City—were used as experimental materials. A widely targeted metabolomic analysis of seeds and seed-removed fruits from both production areas was conducted using ultra performance liquid chromatography tandem mass spectrometry （UPLC-MS/MS）. Principal component analysis （PCA） and orthogonal partial least squares-discriminant analysis （OPLS-DA） were employed to screen differential metabolites， and KEGG pathway enrichment analysis was performed to elucidate accumulation patterns and functions of the metabolites.Result The widely targeted metabolomics analysis identified a total of 1594 se-condary metabolites from seed-removed fruits and seeds of Fortunella hindsii Swingle from the two production areas； the first principal component （PC1） explained 57.60% for the dataset， and the second principal component （PC2） explained 17.86% for the dataset. 1119 and 1072 differentially metabolites were detected in different tissue parts of the fruits from the two production areas， among which 884 were tissue-specific differential metabolites. The peak areas of flavonoids and terpenoids in seed-removed fruits from the two production areas were significantly higher than those in seeds （P<0.05， the same below）； the peak areas of lignans， coumarins， and quinones were significantly higher in seeds than those in seed-removed fruits. KEGG pathway enrichment analysis indicated that the tissue-specific differential metabolites in tissue parts of fruits from the two production areas were enriched in the anthocyanin biosynthesis pathway. In the 33 core differential metabolites were 10 alkaloids， 7 flavonoids， 12 lignans and coumarins， 2 phenolic acids， and 2 other compounds. Among these， 6 core differential metabolites were consistently highly expressed in the seed-removed fruits from the two production areas， including luteolin-6-C-glucoside-7-O-rhamnoside， orientin-2''-O-rhamnoside， luteolin-8-C-glucoside （orientin）. Thereby， 24 geographical-specific differential metabolites were identified： samples of seed-removed fruits and seeds from Yongchun County had 8 and 11 geographical-specific differential metabolites， respectively； samples of seed-removed fruits and seeds from Songxi County had 3 and 2 geographical-specific differential metabolites， respectively.Conclusion Differences in secondary metabolites of Fortunella hindsii Swingle fruits are greater between tissue parts than between geographical origins. Seed-removed fruits are primarily enriched with flavonoids and terpenoids， while seeds are mainly enriched with defensive metabolites such as alkaloids， lignans， and coumarins. A total of 24 geographical-specific differential metabolites between Yongchun County and Songxi County are identified through identification.