This study analyzed the overall nutritional composition of 87 cherry tomato varieties and evaluated the antioxidant, hypoglycemic, and hypolipidemic activities of the top 30 varieties with excellent overall quality. In addition, the phenolic metabolic characteristics of cherry tomatoes were determined via phenolic metabolomics, and the bioactive module "phenolic-DPPH" was identified. There was extensive interspecies variation in total soluble solids, titratable acid, lycopene, chlorophyll, γ-aminobutyric acid, total phenolics, total flavonoids and multivitamins, and different color groups presented unique nutritional compositions. The comprehensive nutritional value of the 56 varieties is greater than that of the Millennium variety. Phenolic substances are closely related to DPPH free radical scavenging activity. A total of 484 phenolic substances were identified, among which 5'-methoxymatairesinoside and 6-hydroxykaempferol-7,6-O-diglucoside are key antioxidant components. Our research provides valuable resources and insights for the selection of functional cherry tomato varieties and the identification of phenolics with important biological activities.