Intraspecific grafting with selected scions and rootstocks has been employed to enhance the secondary metabolites of tea leaves. However, the metabolic shift of secondary metabolites between the scion and rootstock is unknown. In this work, we used Zijuan, a representative purple tea cultivar, as the rootstock and used Yuncha1, a national protected tea cultivar, as the scion. By non-targeted metabolomic analysis, we identified that grafting led to an obvious shift of secondary metabolites between the scion, rootstock, and un-grafted tea leaves. The shifting pattern was driven by the abundance gap of metabolites between the two species. Metabolites lower in the scion-giving plants would be enhanced after grafting while metabolites higher in the scion-giving plants would be decreased. Similarly, metabolites higher in the rootstock-giving plants would be reduced while metabolites lower in the rootstock-giving plants would be increased. Importantly, we found that grafting significantly enhanced the accumulation of flavonoids, the vital component of secondary metabolites for the flavor quality, purple color, and health-beneficial effect of Zijuan tea. Via transcriptomics, we found that the key biosynthetic genes DFR and EC 1.1.1.238 for synthesizing flavonoids were significantly enhanced in rootstock compared with non-grafted Zijuan. Concurrently, ANS for the biodegrading of flavonoids was significantly suppressed in rootstock compared with non-grafted Zijuan. These results reveal the mechanism of metabolic shift of key secondary metabolites during grafting. In addition, we found that the shift after grafting possessed no significant influence on bacterial community diversity but grafting slightly enhanced the fungal community diversity of scions. We found that the shift in fungal community diversity was driven by rootstocks with the higher fungal community diversity. This study systematically reveals the shift of secondary metabolites and fungal community diversity for the first time, which provides a novel and comprehensive understanding and theoretical basis for plant breeding using grafting.