Salt stress has a major effect on the quality and yield of crops, and many transcription factors (TFs), such as WRKY, NAC, and ERF TFs have been shown to participate in the regulation of salt stress. Squamosa promoter binding protein-like (SPL) TFs play a role in plant floral organ development, metal ion responses and disease resistance. However, the precise function of SPL TFs in regulating the salt stress in plants remains unclear. In this study, we investigated the mechanism by which SPL TFs regulate salt stress in apple (Malus domestica). Overexpression of MdSPL13B in apple calli revealed that it positively regulated salt stress. The heterologous transformation of MdSPL3B also resulted in significant salt tolerance in Arabidopsis and tomato. Subsequently, a yeast two-hybrid assay showed that MdSPL13B could interact with MdNAC29 and MdPYL4, which was further confirmed by the bimolecular fluorescence complementation assay. Additionally, overexpression of MdNAC29 and MdPYL4 in apple calli, Arabidopsis and Nicotiana benthamiana plants indicated that MdNAC29 negatively regulated salt tolerance and that MdPYL4 positively regulated salt tolerance. Furthermore, the yeast one-hybrid, electrophoretic mobility shift assay and dual-luciferase assay showed that MdSPL13B could enhance salt tolerance by activating MdWRKY100 in apple. In conclusion, our findings enhance the understanding of how MdSPL3B and its target gene regulate salt tolerance in apple, and have implications for the breeding of salt-tolerant apple.