Soil salinity is a major global challenge affecting agricultural productivity and food security. This study explores innovative strategies to improve salt tolerance in soybean (Glycine max), a crucial crop in the global food supply. This study investigates the synergistic effects of S-nitroso glutathione (GSNO) and silicon on enhancing salt tolerance in soybean (Glycine max). Two soybean cultivars, Seonpung (salt-tolerant) and Cheongja (salt-sensitive), were analyzed for various physiological, biochemical, and genetic traits under salt stress. The results showed that the combined GSNO and Si treatment significantly improved several key traits, including plant height, relative water content, root development, nodule numbers, chlorophyll content, and stomatal aperture, under both control and salt stress conditions. Additionally, this treatment optimized ion homeostasis by enhancing the Na/K ratio and Ca content, while reducing damage markers such as electrolyte leakage, malondialdehyde, and hydrogen peroxide. The stress-responsive compounds, including proline, ascorbate peroxidase, and water-soluble proteins, were elevated under stress conditions, indicating improved tolerance. Gene expression analysis revealed significant upregulation of genes such as GmNHX1, GmSOS2, and GmAKT1, associated with salt stress response, while GmNIP2.1, GmNIP2.2, and GmLBR were downregulated in both varieties. Notably, the salt-sensitive variety Cheongja exhibited higher electrolyte leakage and oxidative damage compared to the salt-tolerant Seonpung. These findings suggest that the combination of GSNO and silicon enhances salt tolerance in soybean by improving physiological resilience, ion homeostasis, and stress-responsive gene expression.