Tomato (Solanum lycopersicum) is among the most important vegetables across the world, but cold stress usually affects its yield and quality. The wild tomato species Solanum habrochaites is commonly utilized as rootstock for enhancing the resistance against abiotic stresses in cultivated tomato, especially cold resistance. However, the underlying molecular mechanism remains unclear. In this research, we confirmed that S. habrochaites rootstock can improve the cold tolerance of cultivated tomato scions, as is revealed by growth, physiological and biochemical indicators. Furthermore, transcriptome profiling indicated significant differences in the scion of homo- and hetero-grafted seedlings, including substantial changes in jasmonic acid biosynthesis and signaling, which were validated by RT-qPCR analysis. S. habrochaites plants had a high basal level of jasmonate, and cold stress caused a greater amount of active JA-Ile in the S. habrochaites hetero-grafts. Moreover, exogenous JA enhanced while JA inhibitor decreased the cold tolerance of tomato grafts. The JA biosynthesis defected mutant (spr8) also showed increased sensitivity to cold stress. All of these results demonstrated the significance of JA in the cold tolerance of grafted tomato seedlings with S. habrochaites rootstock, suggesting a future direction on characterization of natural variation involved in S. habrochaites rootstock-mediated cold tolerance.