To explore the effect of grafting and jasmonic acid on root knot nematode disease, and determine the function of jasmonic acid during grafting on root knot nematode resistance, JA biosynthetic mutant (spr2 plants) and JA-overexpression transgenic plants (35S::PS plants) of tomato were used as rootstocks, wild type of autologous grafting plants as a control, the resistance to root knot nematode between various varieties and the result of grafting on soil microorganism were analysed. The results showed that a total microorganism quantity in spr2 was significantly less than that in 35S::PS plants. Grafting on different rootstocks combinations of WT/ spr2, WT/35S made soil microbial aggregates more than WT/WT. Furthermore, the amount of fungi, actinomyces, and bacteria in grafted plants of WT/35S::PS, was more than WT/WT with a significant difference. Above results suggested that the grafting and jasmonic acid synthesis changed the rhizospheric microorganism amount and composition of tomato, increased the amount of beneficial microorganism, thereby improving the resistance to root knot nematode.