<p>Clarifying the morphological, physiological and molecular mechanisms of rice seedlings in response to salt stress is essential for improving salt tolerance and rice yield. Here, we systematically analyzed the responses of Nipponbare seedlings to salt stress using a two-stage approach. First, NaCl concentration treatments (0–170 mM) revealed a concentration-dependent inhibition of seedling growth. Then, NaCl treatments for 0, 6, and 12&#xa0;h at the critical concentration (90 mM) were conducted to characterize short-term physiological responses. Transcriptome analysis showed temporally specific transcriptional patterns, with 20 salt stress-related co-expression modules identified. Notably, the MEblue module correlated strongly with superoxide dismutase (SOD) (<i>r</i> = 0.93) and peroxidase (POD) (<i>r</i> = 0.9) activities, while the MEpink module was strongly correlated with H₂O₂ content (<i>r</i> = 0.92). Core hub genes (<i>OsSAMS1</i>, <i>ADK2</i>, et al.) were screened from these modules. This study established the critical salt-tolerance concentration of Nipponbare seedlings, characterized their dynamic physiological responses to short-term salt stress, identified the primary antioxidant pathways, and screened potential regulatory genes, thereby providing gene targets and a theoretical basis for understanding salt tolerance mechanisms in rice seedlings.</p>