Abstract Limonoids, a group of highly oxygenated bioactive triterpenoid components, are abundant in citrus. In the present study, a comprehensive metabolomic analysis of limonoids was performed among the flavedo, albedo, segment membrane, juice vesicles, and seeds of pummelo by using Quadrupole-Orbitrap UHPLC-MS/MS. As a result, 21 limonoids were identified in the five tissues and their MS/MS fragmentation characteristics were elucidated. Significant positive correlations were found between juice vesicles and seeds as well as between albedo and segment membranes in limonoid metabolism. Seeds contained fourteen abundant limonoids, while by contrast the flavedo only accumulated three major limonoids (limonin, casimirolide and limonin A-ring lactone). Furthermore, a series of potential biomarkers were developed for limonoid characterization in different tissues or parts. Overall, our results reveal the structural diversity of limonoids and their tissue distribution in pummelo fruit, and lay a foundation for further development and utilization of limonoid metabolites of citrus species.