Vegetable grafting has become an important method for developing resistance to biotic and abiotic stresses and increasing potential yield in agronomic practice. To determine the effects of grafting on tomato taste, we examined the cultivated tomato ‘Moneymaker’ and the wild tomato Solanum pimpinellifolium, which have different fruit weights and qualities, to investigate the effect of grafting on sugars, acids, and volatiles in single-head and double-head grafted plants using GC-MS and LC-MS. We observed that the contents of sugars, acids and volatiles in heterografted tomato pericarps are influenced by rootstocks. Different metabolites exhibit distinct responses to the rootstock and might be associated with rootstock-scion interactions. Comparison of the metabolites in the heterogeneous fruit of the single- and double-head grafted plants indicates that the grafting method also influences the metabolic changes in grafted plants. Moreover, we also identified numerous mobile transcripts and determined that the mobile mRNAs are associated with metabolic processes in tomato leaves. Our work helps to elucidate the effect of genotype and graft method on fruit quality and may provide a basis for future research on rootstock breeding and selection in plants.