Plant salt tolerance is a complex mechanism, and different plant species have different strategies for surviving salt stress. In the present study, we analyzed and compared the morphological and physiological responses of two willow species (Salix linearistipularis and Salix matsudana) from different habitats to salt stress. S. linearistipularis exhibited higher seed germination rates and seedling root Na+ efflux than S. matsudana under salt stress. After salt treatment, S. linearistipularis leaves exhibited less Na+ accumulation, loss of water and chlorophyll, reduction in photosynthetic capacity, and damage to leaf cell structure than leaves of S. matsudana. Scanning electron microscopy combined with gas chromatography mass spectrometry showed that S. linearistipularis leaves had higher cuticular wax loads than S. matsudana leaves. Overall, our results showed that S. linearistipularis had higher salt tolerance than S. matsudana, which was associated with different morphological and physiological responses to salt stress. Furthermore, our study suggested that S. linearistipularis could be a promising tree species for saline-alkali land greening and improvement.