<p>Salt stress significantly impacts agricultural productivity, particularly in China where one-third of irrigated land is affected by soil salinization. Hesperidin (Hes), a natural flavonoid compound, exhibits significant potential in bolstering crop salinity tolerance. This study investigated the optimal concentration of exogenous Hes application for sugar beet seedlings through gradient experiments. Subsequently, the effects of the optimal Hes concentration treatment on photosynthetic parameters, salt-tolerance-related physiological and biochemical indicators, and transcriptomic characteristics of sugar beet seedlings under salt stress were determined. The results indicate that the optimal concentration for exogenous application of Hes in beet seedlings is 100 µM. Under salt stress, Hes can significantly increase seedling biomass and alleviate the adverse effects of salt stress on plant growth, gas exchange, and photosynthesis. Furthermore, treatment with Hes increased the activities of catalase (CAT) and peroxidase (POD), mitigating oxidative damage induced by salt stress. The transcriptome analysis revealed that following Hes treatment, the leaves showed 1,994 differentially expressed genes (DEGs), with gene functions primarily focused on chloroplast and photosynthetic pathways. In contrast, the roots displayed 1,042 DEGs, mainly enriched in pathways associated with taurine and hypotaurine metabolism, nitrogen metabolism, and phenylpropanoid metabolism. Conclusively, Hes significantly enhances the salt tolerance of sugar beet seedlings under salt stress conditions by aiding in the prevention of ROS damage and adjusting the metabolic direction. This study hold significant practical implications for the expansion of sugar beet cultivation areas, the development and utilization of saline-alkali land resources, and the advancement of the sugar beet industry.</p>