Ougan (Citrus suavissima Hort. et Tanaka) is valued for its distinctive sweet–bitter flavor and nutritional properties; however, tissue-resolved metabolic differences between two cultivar forms (seeded and seedless) of Ougan (C. suavissima) remains poorly understood. In this study, a comprehensive UPLC-MS/MS-based metabolomic analysis was conducted on peel (SP and NP), pulp (SF and NF), segment membrane (SM and NM) and seed tissues (SS, from seeded fruit only) of seeded and seedless Ougan fruits. A total of 1333 metabolites were annotated, with flavonoids (48.53%) and phenolics (12.25%) representing the predominant compound classes. Tissues specificity was the primary determinant of metabolic variation, with peel and segment membrane tissue showing relatively high abundance (fold change ≥ 2, |Log₂FC| ≥ 1) of phenylpropanoid- and flavonoid-derived metabolites. Comparative analysis between seeded and seedless tissues revealed significant modulation of phenylpropanoid biosynthesis, flavonoid biosynthesis, phenylalanine metabolism, and related secondary metabolite pathways. Seeded tissues showed a higher relative abundance of selected flavonol glycosides (6-hydroxykaempferol-3,6-O-diglucoside), hydroxycinnamic acid derivatives, and santhocyanin-related compounds, whereas seedless tissues showed higher relative abundance of selected flavanones and malonylated flavonoid glycosides. Seeds were characterized by high limonin content, consistent with limonoid-associated bitterness chemistry. Overall, our findings provide a tissue-resolved metabolomic framework for understanding quality-associated secondary metabolite variation in mature Ougan fruit.