To explore the mechanism of Solanum lycopersicum rootstock function in enhancing salt tolerance of grafted seedlings, we examined the growth, Na+ accumulation, amino acid contents and active oxygen metabolism (ROS) in three grafted seedlings treated with and without 175 mmol·L-1 NaCl conditions. RS grafted seedlings were formed by split grafting using salt-sensitive variety 'Zhongza 9'(S) as scion and salt-tolerant variety 'OZ-006'(R) as rootstock, while the other two experiment materials were the scion self-grafted (SS) and rootstock self-grafted (RR) seedlings. The results showed that NaCl stress significantly increased the salt damage index and Na+ content, concomitantly with substantial decrease in growth rate and chlorophyll content of seedlings. More-over, there were significant differences among the grafting combinations, with an order of SS>RS>RR. NaCl stress significantly increased total amino acid content in the leaves and roots of the grafted seedlings. The amino acid contents were significantly higher than those in the control. There were 9 kinds of amino acid in RR and RS leaves, and 8 kinds in RR and RS roots, with the most significant change in proline. Only 2 and 4 kinds of amino acids in leaves and roots of SS were significantly higher than those in control, respectively. Amino acid contents among three grafted seedlings showed RR>RS>SS under NaCl stress. The contents of amino acid in RR and RS leaves increased by 32.8% and 16.6% compared with SS, and those in RR and RS roots increased by 53.1% and 32.5%, respectively. The changes of ROS were caused by NaCl stress, which enhanced the activities of antioxidant enzymes, the production rate of O2-· and MDA content in both leaves and roots. Among different grafted seedlings, RR had the most prominent increase of antioxidant enzymes activities in leaves and roots, followed by RS, and SS showed the smallest. The active oxygen levels among the three grafted seedlings were show as SS>RS>RR. In summary, rootstock alleviated salt damage of grafted seedlings by inhibiting Na+ transport upward, enhancing amino acid content and antioxidant enzyme activities. The salt tolerance ability showed remarkable difference among three different combinations of rootstock and scion, with a order of RR>RS>SS. Our results suggested that salt tolerance of S. lycopersicum grafted seedlings was mainly affected by the ability of rootstock salt tolerance, followed by scion, and also closely related to the regulation of both amino acid and active oxygen metabolism in seedlings.