Recent studies have shown that the MdDMR6 is a key gene for the control of columnar growing habit. However, there has been no research report on the function of the MdDMR6 gene. In the present study, the columnar apple shoot cultures exhibited better tolerance than that of the standard apple shoot cultures under the salt stress. The expression of MdDMR6 was remarkably induced by the salt stress. Subsequently, the MdDMR6 was transferred into tobacco and apple calli via the Agrobacterium-mediated approach. Functional analysis showed that the overexpressing transgenic tobacco and apple calli displayed salt tolerance and ABA-insensitive phenotype through physiological and biochemical analysis. The MdDMR6 overexpression activated the transcript levels of several genes involved in the ABA-dependent stress genes under the salt condition. These results suggest that the MdDMR6 would increase the plant tolerance to the salt stress via activating or interacting other protein to indirectly activate ABA-dependent pathways.