Background <p>Salt stress is an major abiotic factor limiting yield formation and quality improvement in spring wheat. Previous studies on wheat salt tolerance have mainly focused on shoot injury, ion homeostasis, biomass reduction, or whole-root morphological traits. However, these approaches generally treat the root system as a whole and rarely distinguish whether salt tolerance is associated with the maintenance of deeper roots or with specific anatomical remodeling within root tissues.</p> Methods <p>To address this gap, a high-throughput paper-based cultivation platform was used to assess the shoot phenotypes, root architectural traits, and root anatomical characteristics in 28 spring wheat genotypes under control and salt-stress conditions. Salt tolerance coefficients were calculated for multiple traits and integrated using principal component analysis, membership function analysis, contribution-rate-based weighting, and comprehensive D-value clustering. Genotypes with contrasting salt tolerance were then selected for further comparison of stratified root architecture and root anatomical responses.</p> Results <p>The results showed that salt stress significantly inhibited both shoot and root growth in spring wheat. The first five principal components explained 81.37% of the total variation, and the integrated evaluation framework effectively distinguished genotypic differences in salt tolerance. Plant height, total root length, average root length, cortex/stele area ratio, and lacuna/cortex area ratio were identified as candidate phenotypic and anatomical indicators associated with variation in salt tolerance. Further correlation and stratified root analyses showed that the maintenance of root architecture and anatomical adjustment were significantly associated with shoot growth performance under salt stress. In the deeper root layer, salt-tolerant genotypes maintained relatively more stable root traits, with root surface area reduced by 18.68%–38.61%, whereas the corresponding reductions in salt-sensitive genotypes ranged from 28.57% to 90.00%. Meanwhile, salt-tolerant genotypes exhibited a more coordinated pattern of cortical contraction, stele maintenance, and lacuna adjustment, suggesting that salt tolerance in spring wheat seedlings may be associated with the combined maintenance of deeper roots and anatomical remodeling rather than with a single root structural trait.</p> Conclusion <p>This study advances the evaluation of salt tolerance in wheat by linking whole-plant performance with stratified root architecture and root anatomical organization. The results suggest that salt tolerance in spring wheat seedlings is associated not simply with total root size, but with the coordinated maintenance of deeper roots and anatomical remodeling of cortex, stele, and lacuna tissues. These findings provide a more refined root trait framework for salt-tolerant germplasm screening and root-based improvement of spring wheat.</p>