Melatonin (MT) is an important phytohormone that significantly regulates the growth and development of plants. Previous studies confirmed the effectiveness of MT in improving plant stress tolerance. In this study, annual M9-T337 seedlings were selected as subjects and five treatments were applied: conventional control (CK), in which only half the concentration of Hoagland was applied; Saline-alkali stress treatment (SA, 100 mmol·L-1 Saline-alkali solution); melatonin treatment (MT, CK + 200 μmol·L-1 exogenous MT); Saline-alkali + melatonin treatment (MS, SA + 200 μmol·L-1 exogenous MT); and Saline-alkali stress + melatonin + inhibitor treatment (HS, additional 100 μmol·L-1 p-CPA treatment to MS). The results showed that Saline-alkali stress negatively affected the growth of M9-T337 seedlings by reducing photosynthetic capacity, increasing Na+, promoting reactive oxygen species such as H2O2, and changing the osmotic content and antioxidant system. However, the application of exogenous MT effectively alleviated Saline-alkali damage and significantly promoted the growth of M9-T337 seedlings. It significantly increased plant height, diameter, root length, root surface area, volume and activity. Furthermore, MT alleviated osmotic stress by accumulating proline, soluble sugars, soluble proteins and starch. Furthermore, MT improved photosynthetic capacity by delaying chlorophyll degradation and regulating gas exchange parameters as well as fluorescence parameters in leaves. Furthermore, MT improved the Na+/K+ ratio to reduce ion toxicity by upregulating the expression of Na+ transporter genes (MhCAX5, MhCHX15, MhSOS1, and MhALT1) and downregulating the expression of K+ transporter genes (MhSKOR and MhNHX4). In addition, MT can increase antioxidant enzyme activity (SOD, POD, CAT, AAO, APX and MDH) in the ASA-GSH cycle and increase AsA, GSH and GSSG levels to counteract the accumulation of reactive oxygen species (ROS). such as H2O2 and O2-, reducing oxidative damage. Exogenous MT promotes root growth under salt-alkaline stress by increasing root activity and responding synergistically with IAA, GA3 and ZT to salt-alkaline stress. Our results confirm that MT has the potential to alleviate Saline-alkali stress by promoting root growth, increasing biomass accumulation and photosynthetic capacity, strengthening the antioxidant defense system, maintaining ionic balance, the ascorbate-glutathione cycle and the Osmoregulation facilitates and regulates endogenous hormone levels in M9-T337 seedlings.