Rambutan seed oil presents a promising source of edible vegetable oil. Nevertheless, there is a dearth of studies regarding the metabolite profile of rambutan seed oil. This study comprehensively characterized and compared the metabolite profiles of seed oils from three rambutan cultivars by integrating metabolomics and chemometrics. A total of 544 metabolites were identified. Lipids and terpenoids represent the predominant metabolites. Significant differences in the metabolite composition of rambutan seed oil were observed among the varieties. BR-7 contained high levels of flavonoids, BR-4 had high levels of organic acids and derivatives, and BR-5 had the lowest levels of amino acids and derivatives. Forty-two differential metabolites were identified through chemometric modeling. Isoricinoleic acid displayed positive correlations with the majority of differential metabolites. Furthermore, KEGG enrichment analyses revealed that alpha-Linolenic acid metabolism predominated among the metabolic pathways. Overall, the metabolite profiles distinguish the seed oils of these three rambutan varieties, potentially opening new avenues for researching the functionality of rambutan seed oil.