Omics is the analysis of large amounts of data representing an entire set of molecules. It is the study of genome, transcriptome, proteome, and metabolome, and is further classified into other fields, such as epigenomics, lipidomics, glycomics, foodomics, and nutriomics. The latter is a branch of food science incorporating nutritional studies leading to data that support consumers’ well-being and improve health. Countless combinations of omics approaches have been used for the mining of novel bioactive compounds from natural products. Cutting-edge, large-scale omics analyses have revolutionized medical research to reveal markers in diseases and potential bioactive compounds for therapeutic purposes. Current efforts and progress in comparative nutriomic research are the main driving force for future nutriomic applications to derive personalized formulation based on systems biology. The omics platforms and various bioinformatic tools discussed have the potential to shed light on the complex relationship between dietary nutrition and metabolism for health improvement.