A foodomics approach was employed to systematically characterize and compare the quality parameters, antioxidant activity, minor-components, fatty acid composition, and lipid profiles of the seed oils from the three most popular rambutan varieties in China. The total lipid content ranged from 23.40 to 25.77 g/100 g. The fatty acids 9cC18:1 (39.84%-40.92%) and C20:0 (28.45%-30.23%) were identified as the dominant ones, which are uncommon among higher plants. All oil samples exhibited low AI and TI values. BR-7 exhibited the highest levels of squalene (21.48 mg/kg), cholesterol (144.43 mg/kg), and tocopherol (17.42 mg/kg), and the lowest levels of polyphenols (24.21 mg GAE/kg). Additionally, a total of 807 lipid species were identified, with TAG, DGTS, and PE being the predominant ones. Multivariate statistical analyses revealed significant variations in lipid profiles among the varieties, particularly in glycerophospholipids and sphingolipids. Fifty-seven distinct lipids were identified as potential markers for distinguishing between rambutan varieties. Furthermore, a hypothetical scenario was developed by linking relevant lipid metabolism pathways. These findings establish a theoretical framework for comprehending rambutan seed oil in depth and unlocking its high-value potential.