The quality of agricultural products is determined by the nutritional composition. Many edible oils and essential oils are enriched with bioactive compounds so that the evaluation of individual oils is actively engaged in research. In the current study, a high-throughput untargeted metabolic profiling was done on 35 edible and essential oils. Based on LC-MS/MS analysis, a total of 495 secondary metabolites and 564 lipids were structurally identified. Multivariate statistics and cheminformatics demonstrated the global characterization of oils. The PERMANOVA demonstrated that the origin, the extraction method and the phylogenetic distance of the oils explained a total of 77% of the total variation in the metabolic profiles. Firstly, the origin of the oils discriminated the oils into three clusters based on OPLS-DA model. The oils in Cluster A and B were from Asia and Europe. They were rich in hydrophilic metabolites compared to the oils in cluster C. A subsequent multivariate statistics identified the key metabolites that majorly discriminated the cluster A and B from cluster C. C10H8O3, FA 20:0, methyl cinnamate and FA 22:5;0 were highly correlated with cluster A. FA 10:0;OH, FA 15:1;2O, FA 18:3;3O and FA 20:3;4O were highly correlated with cluster B. A subsequent PCA model discriminated oil X, Y and Z from other oils based on the extraction method of the oils. The oil X, Y and Z were extracted by the mechanical press while the other oils were extracted by steam distillation. The PCA model also discriminated bio-active oils based on their functional metabolites. The oil   and   showed a high anti-oxidant activity compared to other oils in cluster A. The oil   showed a higher anti-inflammatory activity compared to the other oils in cluster B. Next, the phylogenetic distance and the metabolomic phenotypes of the oils were analyzed. The oils in Cluster C and Cluster D had the closest genetic distance between them, but their metabolomic phenotypes were distinctively discriminated by the t2 vector. The oils in cluster C had higher abundance of organic oxygen compounds and phenylpropanoid and polyketides than oils in Cluster B. This study enabled an integrative characterization of various edible and essential oils based on the origin, extraction method and the phylogenetic distance of the oils.