The compositions and contents of soluble sugars highly determine the flavor and quality of fleshy fruits. In the present study, we found that the overexpression of transcription factor MdWRKY126 localized on the nucleus enhanced sucrose concentration while decreased fructose and glucose concentration in transgenic apple calli and ripening tomato fruits. To comprehensively understand the effects of the MdWRKY126 on the content of various soluble sugars in apple and tomato fruits, enzyme activities and related essential genes associated with the sugar metabolism and transportation pathway in MdWRKY126-overrexpressed apple and tomato lines were analyzed. The results indicated that the overexpression of MdWRKY126 upregulated sucrose phosphate synthase (SPS) activity and the gene expression levels of SPS and sucrose transporter SUT, which was conducive to a large accumulation of sucrose in fruit cells. Meanwhile, MdWRKY126 overexpression downregulated the activity of enzymes involved in sucrose decomposition including cell wall invertase (CWINV), sucrose synthase (SUSY) and the corresponding gene expressions, as well as inhibited the expression levels of hexose transporter (HTs) and tonoplast sugar transporter (TSTs) that transport hexose into vacuoles, resulting in a reduced hexose level in apple calli and tomato fruit. These findings enrich our understanding of the metabolism and regulation of soluble sugars in apple fruits.