Understanding metabolic shifts and the regulatory network during fleshy fruiting in fruit crops is highly valuable for the design of crop improvement targeting better plant growth, fruit yield,stress tolerance, fruit shelf-life, nutritional quality, and health benefits.The “fruit omics” approach, which is an integrative omics analysis focusing on fruit development and ripening, has been highly developed for tomato species after its genome was sequenced.With the current advantage of next-generation sequencing for transcriptomics and the significant development of mass spectrometry-based metabolomics, tomato fruit omics studies have provided many key insights on metabolic shifts and networks during fruit ripening with fruit organ specificities.These studies have focused on primary metabolites as well as “specialized (secondary) metabolites,” which are phytochemicals with bioactivities that can confer health benefits and act as stress protectants, because of their usability in crop improvement.