<p>Grafting is a common agronomic strategy to improve growth, stress tolerance, and fruit quality in tomato. However, the molecular and metabolic mechanisms by which rootstocks regulate tomato fruit nutritional and flavor quality remain largely unclear. In this study, the tomato cultivar HZ504 was used as the scion and grafted onto three rootstocks (JZ, TLBM, JB), with self-grafted HZ504 as the control. Agronomic trait analysis showed that JZ rootstock significantly increased fruit number per plant and total soluble solids content. Integrated transcriptomic and metabolomic analyses revealed that JZ rootstock broadly altered the transcriptome and metabolome of scion fruits. Metabolites such as flavonoids, phenolic acids, terpenoids, and amino acids, all closely linked to flavor and nutrition, were elevated. On the transcriptome side, differentially expressed genes were mainly enriched in photosynthesis, starch and sucrose metabolism, and the phenylpropanoid/flavonoid biosynthesis pathways. At the pink ripening stage, JZ specifically upregulated key flavonoid pathway genes in a ripening-dependent manner, tightly correlating with increased flavonoid accumulation. Together, these results indicate that JZ rootstock enhances tomato yield and quality by reorganizing transcription and metabolic flux, particularly toward flavonoid biosynthesis. This work provides a practical basis for rootstock selection and sustainable production of high-quality tomatoes.</p>