Salt stress has strongly impacted the long-term growth of eco-friendly farming worldwide. By targeting the oxidative stress induced by salt, the utilization of biomass-derived carbon dots (CDs) that possess high-efficiency antioxidant properties, are nontoxic, and have excellent biocompatibility represents a viable and effective approach for enhancing the salt tolerance of plants. In this study, we blended magnesium oxide nanoparticles with carbon sources derived from durian shells to construct Mg-doped carbon dots (Mg-CDs) through a hydrothermal reaction. We demonstrated that the foliar application of 150 μg/mL Mg-CDs to rice plants after treatment with 100 mM salt effectively increased the plant height (9.52%), fresh weight (22.41%), dry weight (33.33%), K+ content (21.46%), chlorophyll content (36.21%), and carotenoid content (16.21%); decreased the malondialdehyde (MDA) (9.43%), Na+ (25.75%), H2O2 (17.50%), and O2•- contents (37.99%); and promoted the photosynthetic system and antioxidant activity. Transcriptome analysis revealed that Mg-CD pretreatment triggered transcriptional reprogramming in rice seedlings. The enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes pathways based on trend groups of gene expression patterns of Profile 8 and Profile 15 indicated that priming with Mg-CDs activated stress signaling- and defense-related pathways, such as metabolic pathways, biosynthesis of secondary metabolites, and photosynthesis pathways. These activations subsequently prompted the expression of genes related to the mitogen-activated protein kinase signaling pathway, hormone signal transduction, the oxidative stress response, and the photosynthetic system. This study demonstrated that the use of Mg-CDs represents a potential strategy to increase plant salt tolerance, creating the possibility for the regulation of crop salinity stress and offering valuable advancements in sustainable agriculture.