Soil remediation for cadmium (Cd) toxicity is essential for successful tobacco cultivation and production. Melatonin application can relieve heavy metal stress and promote plant growth; however, it remains somewhat unclear whether melatonin supplementation can remediate the effects of Cd toxicity on the growth and development of tobacco seedlings. Herein, we evaluated the effect of soil-applied melatonin on Cd accumulation in tobacco seedlings, as well as the responses in growth, physiological and biochemical parameters, and the expression of stress-responsive genes. Our results demonstrate that melatonin application mitigated Cd stress in tobacco, and thus promoted plant growth. It increased root fresh weight, dry weight, shoot fresh weight and dry weight by 58.40%, 163.80%, 34.70% and 84.09%, respectively, compared to the control. Physiological analyses also showed significant differences in photosynthetic rate and pigment formation among the treatments, with the highest improvements recorded for melatonin application. In addition, melatonin application alleviated Cd-induced oxidative damage by reducing MDA content and enhancing the activities of enzymatic antioxidants (CAT, SOD, POD and APX) as well as non-enzymatic antioxidants (GSH and AsA). Moreover, confocal microscopic imaging confirmed the effectiveness of melatonin application in sustaining cell integrity under Cd stress. Scanning Electron Microscopy (SEM) observations illustrated the alleviative role of melatonin on stomata and ultrastructural features under Cd toxicity. The qRT-PCR analysis revealed that melatonin application upregulated the expression of photosynthetic and antioxidant-related genes, including SNtChl, q-NtCSD1, NtPsy2 and QntFSD1, in tobacco leaves. Together, our results suggest that soil-applied melatonin can promote tobacco tolerance to Cd stress by modulating morpho-physiological and biochemical changes, as well as the expression of relevant genes.