Soybean is a major source of plant-based protein and vegetable oil, but its productivity is severely limited by soil salinity. Transcription factors including NAC family play pivotal roles in regulating stress-responsive pathways. Here, we identified and characterized a salt-induced NAC transcription factor, GmNAC03, in soybean. Overexpression of GmNAC03 significantly improved salt tolerance at both the germination and seedling stages. Physiological analyses revealed that antioxidant enzyme activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were elevated in GmNAC03 transgenic lines, accompanied by reduced malondialdehyde (MDA) accumulation, indicating enhanced oxidative stress resistance. To further explore its regulatory mechanisms, RNA-seq analysis was performed, which showed that GmNAC03 overexpression affected pathways related to amino acid metabolism, particularly glutamine and aspartate family amino acid biosynthesis, as well as phenylpropanoid biosynthesis. Differentially expressed genes were enriched in alanine, aspartate, and glutamate metabolism, suggesting a role for GmNAC03 in metabolic reprogramming under salt stress. Together, these findings demonstrate that GmNAC03 functions as a positive regulator of salt tolerance in soybean by modulating antioxidant defense and amino acid metabolic pathways. This work provides new insights into the molecular basis of NAC-mediated stress adaptation and offers a potential target for breeding soybean varieties with enhanced salinity resistance.