Taking two tomato cultivars Zhongza No. 9 and Jinpengchaoguan as test objects, a hydroponic experiment was conducted to study the effects of exogenous spermidine (Spd) on the tomato seedling nitrogen metabolism and main mineral elements contents under saline-alkali stress. Under the stress, the seedling dry biomass decreased significantly, and the plant growth was inhibited. The activities of nitrate reductase (NR), glutamine synthetase (GS), and glutamate synthase (GOGAT) and the contents of nitrate nitrogen (NO3(-)-N) and total N, K, Ca2+, and Mg2+ in leaves and roots decreased significantly, while the contents of ammonium nitrogen (NH4(+)-N), and Na+ had a significant increase. The activity of glutamate dehydrogenase (GDH) in the leaves of the two cultivars and in the roots of Zhongza No. 9 increased significantly, but that in the roots of Jinpengchaoguan had less change. The total P content in the leaves of the two cultivars decreased significantly, while that in the roots of Jinpengchaoguan and Zhongza No. 9 had a significant increase and less change, respectively. Applying exogenous Spd increased the assimilation of NH4+ by the plants through increasing the NR, GS and GOGAT activities, alleviated the nitrogen metabolic disturbance caused by the saline-alkali stress, and further, promoted the absorption, release, or transportation of P, K, Ca, Mg, and Na in different organs, maintained a proper balance among the nutrients, and improved the plant saline-alkali resistance. Zhongza No. 9 was more sensitive to the saline-alkali stress than Jinpengchaoguan, and the alleviation effect of exogenous Spd on the nitrogen metabolic disturbance and nutritional out-of-balance of Zhongza No. 9 was more obvious.