Plant biologists aim for the genetic improvement of barley adaptation to salinity stress. This study was designed to explore the natural variation of responsive physiological and agronomic traits in a diverse spring barley panel under salt-affected soil and the application of selenium nanoparticles (Se-NP) during the vegetative phase. Significant phenotypic variation was detected among the accessions in response to salt stress. Application of 1 mM Se-NP enhanced thousand kernel weight (TKW) by 28% while decreasing the Na+ contents in the flag leaves by 53% . The genomic analysis lead to having in total, of 146 associated SNPs with salt-responsive traits using 19 K SNPs in a genome-wide association study analysis. High significant SNPs were located within or near candidate genes which are potentially involved in the stress tolerance mechanism via enhancing the expression of Na+/H+ antiporters and tonoplast H+-ATPase. The candidate genes include HORVU.MOREX.r3.2HG0184880 and HORVU.MOREX.r3.2HG0199370 that encodes sulfite reductase and anthocyanidin reductase, respectively, confirming the crucial role of Se-NP in improving barley salt tolerance. We further showed the allelic variation inside the genes associated with traits under Se-NP leads to enhancing the accumulation of N, P, K+, ion homeostasis, antioxidant metabolism, nitrogen uptake, and ultimately grain yield. This study provides desirable alleles for salt tolerance in barley breeding strategies.