Low available magnesium (Mg) content in soils is prevalent across China"s primary lemon-producing regions, leading to frequent Mg deficiency symptoms in lemon plants and compromising fruit yield and quality. To investigate the differential nutrient uptake in lemon saplings under Mg-deficient stress and identify Mg-tolerant rootstocks, this study employed a hydroponic sand culture experiment using lemon saplings grafted ontoSTrifoliate orange andSC35 citrange rootstocks. Two Mg treatments were applied: adequate Mg supply (1 mmol/L MgSO4.7H2O) and Mg-deficient stress (0 mmol/L). After 180 days of cultivation, nutrient concentrations and translocation coefficients across various tissues were quantified. Results demonstrated that under adequate Mg supply,SP. trifoliata-grafted saplings exhibited significantly higher Mg uptake and utilization efficiency compared to C35 citrange-grafted saplings, along with superior Mn and Cu accumulation capacity. Mg deficiency reduced N translocation coefficients in both rootstock systems, while C35 citrange-grafted plants demonstrated higher Mg utilization efficiency. However, C35 citrange rootstock displayed impaired translocation capacity for Ca, Fe, Mn, and Zn. Notably, Mg-deficient conditions markedly increased Mn absorption inSP. trifoliata-grafted saplings, posing potential Mn toxicity risks. Comprehensive analysis revealed that C35 citrange rootstock offers distinct advantages for "Yunning No.1" cultivation under Mg-deficient but otherwise nutrient-sufficient conditions, whereas traditionalSP. trifoliataSrootstock proves more suitable for multi-nutrient-deficient environments.