Both magnesium (Mg) and nitrogen (N) play many important roles in plant physiological and biochemical processes. Plants usually exhibit low nitrogen utilization efficiency (NUE) under Mg deficiency conditions, but the mechanisms by which Mg regulates NUE are not well understood. Herein, we investigated biomass, nutrient uptake, sorbitol and sucrose transport, and relative gene expression in apple seedlings under various concentrations of Mg and N treatments in hydroponic cultures. We first observed that low Mg supply significantly limited plant growth and N, Mg concentrations. Increasing the supply of N, but not Mg, partially alleviated the inhibition of plant growth under low Mg stress, which indicated that Mg deficiency had a negative impact on plant growth because it inhibits N absorption. Moreover, we found that the expression of nitrate transporter genes MdNRT2.1 and MdNRT2.4 was significantly downregulated by low Mg stress, and sufficient Mg significantly promoted sucrose and sorbitol synthesis and transport from leaves to roots by regulating relevant enzyme activity and genes expression. Further experiments showed that exogenous sorbitol can rapidly restore MdNRT2.1/2.4 expression and nitrate uptake under low Mg availability, suggesting that Mg may regulate MdNRT2.1/2.4 expression by regulating more sorbitol transport to roots. Taken together, Mg promoted sorbitol synthesis and transport into roots, thus upregulating the expression of MdNRT2.1/2.4 and increasing the absorption of nitrate.