Salicylic acid (SA) is a vital phytohormone that can mitigate the detrimental effects caused by abiotic stress in plants; however, these effects vary with SA concentrations, plant species and stress types. Although sunflowers can be cultivated on saline-alkali soil, they remain susceptible to salt stress, especially at the seedling stage. Therefore, we aimed to explore the role of SA in improving salt stress tolerance in sunflowers. Here, we conducted physiology and transcriptomic analyses to assess the effects of four SA concentrations applied through foliar spraying on sunflower seedlings under salt stress. Initially, the height and stem diameter were impeded, and the chlorophyll fluorescence parameters (such as Fv/Fm, Fv/Fo, and PIabs) decreased, but the antioxidant enzyme activity and malondialdehyde and glutathione contents increased when the seedlings exposed to salt stress (250 mM NaCl); meanwhile, the levels of most physiological indices (including plant growth, chlorophyll fluorescence, and reactive oxygen species) significantly recovered after spraying four concentrations of SA solution. Furthermore, the differentially expressed genes identified from transcriptome analysis were mainly involved in photosynthesis, plant hormone signaling, MAPK pathway, and secondary metabolite biosynthesis, which may contribute to the SA-induced response under salt stress. The key genes and TFs crucially involved in the response to salt stress and mitigating its detrimental effects were identified through K-means clustering and WGCNA. We may infer that SA can activate the self-regulatory system, thereby mitigating oxidative damage and enhancing photosynthesis and salt tolerance in plants. Overall, our results demonstrate that 1.0 mM SA is the most effective concentration for alleviating salt stress in sunflowers. This study provides initial insights into the ability of SA to alleviate salt stress and its underlying molecular mechanisms, which is valuable for both field management practices and understanding sunflower tolerance to salinity.