In this study, the regulatory effect of exogenous melatonin on the expression of genes related to the AsA-GSH cycle and nitrogen metabolism in seedlings under NaCl stress was determined; the homology between enzyme genes and similar genes in other species was analyzed by applying different concentrations of exogenous melatonin to rice seedlings under NaCl stress; and the morphology and physiological indicators of seedlings were determined. Exogenous melatonin was found to upregulate the expression of OsGR3, OsGPX1, OsNR2, OsGS1, and OsGOGAT1 in seedlings under NaCl stress, which enhanced the enzyme activities of the AsA-GSH cycle and nitrogen metabolism, ultimately reducing the content of reactive oxygen species (ROS) and improving the photosynthetic rate and nitrogen efficiency. A high homology was found when rice OsGR3, OsGPX1, OsNR2, OsGS1, and OsGOGAT1 were compared with similar genes in Arabidopsis thaliana, Hordeum vulgare, Zea mays, and Sorghum bicolor. Further, the location of the gene on the chromosome, the similar gene structure, GO annotation, and KEGG metabolic pathways were explained by the functions and metabolic processes of OsGR3, OsGPX1, OsNR2, OsGS1, and OsGOGAT1. Overall, our findings indicate that exogenous melatonin participates in the regulation of enzyme gene expression during the AsA-GSH cycle and nitrogen metabolism, ultimately affecting the activities of related enzymes and alleviating the oxidative damage induced by ROS in seedlings.