Grafting is commonly used to enhance the quality and confer biotic or abiotic stress tolerance to plants. There is, however, no clear understanding of how grafted eggplant responds to cold stress. Here, four grafting combinations of eggplant from cold-sensitive line J55 and cold-resistant line J65 were subjected to morpho-physiological experiments and transcriptome sequencing to compare their responses to cold stress. After being subjected to cold stress, a total of 5883,6608,6867 and 5815 differentially expressed genes (DEGs) were identified in J55-J55L0_vs_J55-J55L1 (C0), J55-J65_vs_J55-J65L1 (T2), J65-J55_vs_J65-J55L1 (T1), and J65-J65_vs_J65-J65L1 (C1), respectively. When comparing C0 and C1, there exist 4580 specifical DEGs which were differentially expressed either in C0 or C1 (C0_vs_C1), these DEGs are more likely to induce the difference of the two grafted combinations. There is a total of 5583 specifical DEGs in C0_vs_T1 and 5209 specifical DEGs in C0_vs_T2, respectively. GO functional analysis found specifical DEGs mainly enriched the cell and membrane, catalytic activity, metabolic process, and cellular process, which was the same in comparison to heterografted and self-grafted eggplant in C0_vs_C1, C0_vs_T1 and C0_vs_T2. KEGG analysis showed that the specifical DEGs were mainly enriched in plant hormone signal transduction in C0_vs_C1, C0_vs_T1, and C0_vs_T2. Therefore, we screened ten candidate genes associated with AUX/IAA, salicylic acid and other hormone regulations that were differentially expressed in C0_vs_C1 C0_vs_T1, and C0_vs_T2. We believe that plant hormones play a vital role in regulating the cold tolerance of grafted eggplant. We also found that 22 DEGs enriched in arginine and proline metabolism in comparison to self-and hetero-grafted eggplant C0 and T1, predicted that putrescine biosynthesis plays a certain role in improving the cold resistance of eggplant by heterologous grafting. Meanwhile, by the comparison of specifical DEGs on C0_vs_C1 and C0_vs_T2, the DEGs enriched in a similar KEGG pathway, it is considered that the better cold tolerance of J65 as a scion has a more important effect on the cold resistance of eggplant.