Salinity is a major abiotic stress that threatens crop production and the food supply in saline regions. Salt-tolerant wheat germplasm resources and an understanding of the underlying molecular mechanisms are needed for the breeding of salt-resistant cultivars. In this study, 543 wheat genotypes were used to identify new germplasm resources tolerant to salinity stress in four environments (hydroponic test, pot test, salt pond test, and saline-alkali land test). In total, 14 (hydroponic test) and 19 (other tests) agronomic traits were used to classify the salt tolerance of the examined genotypes, among which Cangmai6005 (CM6005) and Kenong9204 (KN9204) were respectively salt-tolerant and salt-sensitive varieties. The morphological and physiological indices of these two varieties were compared at the bud and seedling stages. The effects of salinity on these varieties were assessed at the transcriptome level. A total of 15,644 genes were differentially expressed in the bud and seedling stages, with more up-regulated genes in CM6005 than in KN9204. These genes were found to be significantly associated with 134 pathways, such as trehalose-related processes, MAPK signal transduction, JA-related pathways, and ABA-related processes, potentially offering insights into the differing salt tolerance observed between CM6005 and KN9204. The analyzed wheat varieties may be potential for breeding new salt-tolerant wheat varieties and for research on the genetic mechanism mediating the wheat response to salt stress.