Background <p>Faba bean (<i>Vicia faba</i> L.) is a crucial cool-season legume crop, which is highly valued for its high protein content and key role in crop rotation systems. Considering the increasing threat of soil salinity and alkalinity globally, it is critical to screen germplasm resources with saline-alkali tolerance in faba bean and to identify the underlying genes.</p> Results <p>In this study, 12 morphological and physiological traits under compound saline-alkali stress conditions were measured to evaluate saline-alkali tolerance of 240 accessions based on principal component analysis. The results showed that biomass-related traits such as fresh weight of shoot and leaf number had relatively high weights in the evaluation of saline-alkali tolerance at the seedling stage, and 38 highly saline-alkali tolerant accessions were identified. A total of 242 SNPs affecting seedling saline-alkali tolerance were identified in a genome-wide association study of 240 faba bean accessions, with 57 SNPs significantly associated with 7 traits and identified by GLM and MLM models. It was found that 10 genes (such as <i>L-GalLDH</i>, <i>ZAT4</i>, <i>NAC82</i>) overlapped with the reported genes related to saline-alkali tolerance or stress resistance by functional annotation of candidate genes, and their elevated expression in tolerant accessions was validated by RT-qPCR. RT-qPCR indicated tissue-specific differential expression between tolerant and sensitive accessions, with most genes showing higher expression in the tolerant line.</p> Conclusions <p>These findings enhance our understanding of the genetic mechanisms governing salt-alkali tolerance in faba bean seedlings and supplies valuable high-tolerance accessions alongside candidate gene resources for breeding programs, thereby laying a solid foundation for subsequent functional validation of these genes.</p>