Plants synthesize a diverse array of secondary metabolites that are important for them to survive and flourish in the natural environments. The root secondary metabolites play an important role in plant microbe interactions, particularly in the plant defenses against pathogenic attacks. Verticillium dahliae the causal agent of Verticillium wilt, often attack the root of eggplants, and causes significant reductions of yield in eggplant (Solanum melongena L.) production where crop rotation is limited. Grafting is considered as an effective method to control this disease. Some wild species eggplants and resistant tomatoes are available for eggplant rootstock. After grafting, the root secondary metabolites could change to resist the V. dahliae stress. Therefore, the regulation of grafting to root secondary metabolism may be one of the disease resistance metabolisms for grafting. Using tomato as rootstock, the effects of grafted eggplant on root secondary metabolites were studied by GC-MS in this paper. The modulation of grafting to root secondary metabolism was discussed by comparing the root secondary metabolites with and without Verticillium dahliae stress. The allelopathic effects of butanedioic acid, dimethyl ester to Verticillium wilt (Verticillium dahllae), seed germination and seedling growth of eggplant in grafted treatment were determined using simulative method. The results showed that grafting affected the secondary metabolism of eggplant roots without V. dahliae stress. The categories and amounts of root secondary metabolites increased, and their relative contents in grafted treatment changed compared with non-grafted treatment. Nine categories and 66 substances in grafted treatment were detected, in which were 4 categories and 33 substances were determined in grafted treatment than in non-grafted treatment. Under V. dahliae stress, the grafted treatment exhibited strong disease resistance. Amang the root secondary metabolites, the relative contents of hydrocarbon and phenol and acohol in grafted treatment were increased by 3.25% and 0.07% compared with non-grafted treatment, while benzene, indene and fatty acid ester were decreased by 2.62%, 0.26% and 0.07%, respectively. Amine was detected only in grafted treatment, but not fluorine. For grafted treatment, after inoculating V. dahliae, the contents of benzene, indene, phenol, acohol and amine were increased by 22.07%, 1.72%, 1.21% and 0.34%, respectively, but hydrocarbon and fatty acid ester decreased by 1.28% and 21.75%, respectively. There was no ketone, carbazole and fluorine in grafted treatment under V. dahliae stress. Butanedioic acid, dimethyl ester presented only in grafted treatment after inoculating V. dahliae, and was the most distinct. Butanedioic acid, dimethyl ester enhanced the disease resistance of eggplant and inhibited the mycelium growth of V. dahliae. And it improved the seed germination and seedling growth of eggplants. At the concentration of 1 mmol/L, the improvements were the best. It indicates that grafting can affect the composition of eggplants by using tomato as rootstock.