Objective This study aimed to compare the composition and relative contents of volatile components between whole and seed-removed fruits of Fortunella hindsii, screen for the key differential substances, elucidate the material basis for the differentiation of odor and efficacy, and provide a theoretical basis for the diversified, precise, and high-value utilization of F. hindsii germplasm resources.

Method Headspace gas chromatography-mass spectrometry (HS-GC-MS) was employed to determine the volatile components of two types of low-temperature dried whole and seed-removed fruits of F. hindsii. The relative contents of each component were calculated using the peak area normalization method. Multivariate statistical methods, including principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), variable importance in projection (VIP), and hierarchical clustering analysis (HCA), were applied for data interpretation.

Result A total of 39 volatile components were detected from two types of whole fruit and seed-removed fruit of Fortunella hindsii. Terpenoids were the most abundant in both variety and content, among which monoterpenes showed the highest relative content, followed by sesquiterpenes. Five common volatile components were identified across the four sample groups, namely β-pinene, D-limonene, β-copaene, (+)-bicyclogermacrene, and γ-terpinene. Among them, β-pinene exhibited the highest relative content in all four groups, while β-copaene was the second most abundant volatile component in the two seed-removed fruit groups. In addition, 16 unique volatile components were detected. Principal component analysis (PCA) revealed that treatment effect was the primary driving factor causing differences in volatile profiles. The orthogonal partial least squares discriminant analysis (OPLS-DA) model exhibited good fitting performance (R²Y = 0.999, Q² = 0.998) and effectively distinguished between whole fruit and seed-removed fruit treatments. Using dual screening criteria of VIP value > 1.00 and fold change (FC) ≥ 2.0 or ≤ 0.5, 17 key differential components were identified, which formed visually distinct reverse-differentiation blocks in hierarchical clustering heatmaps. The results of PCA, OPLS-DA, and hierarchical cluster analysis (HCA) were highly consistent, all effectively differentiating the volatile profiles of whole fruit and seed-removed fruit samples.

Conclusion There were significant differences in the composition and relative content of volatile components between whole and seed-removed fruits of F. hindsii. The whole fruit was characterized by monoterpenes (e.g., D-limonene) as its core constituents, whereas the seed-removed fruit was marked by sesquiterpenes (e.g., β-caryophyllene and elemenes) as its signature substances. Seed removal was identified as the primary factor responsible for the differences in volatile profiles. These findings provide a scientific basis for elucidating the differentiation mechanism between the "odor–efficacy" profiles of whole fruit and seed-removed fruit, as well as for the development of functional products.