Nitrogen (N) is essential for the physiological metabolism, growth, and development of plants. Plants have evolved a complex regulatory network for the efficient regulation of N uptake and utilization to adapt to fluctuations in environmental N levels. However, the mechanisms underlying the regulation of N absorption and utilization in apple remain unclear. Here, we identified MdILR3 (IAA-LEUCINE RESISTANT3) as an upstream regulator of MdNRT2.4 through yeast one-hybrid (Y1H) screening. MdILR3 overexpression significantly up-regulated the expression of MdNRT2.3/2.4 and MdNIA1, resulting in an increase in nitrate content and nitrate reductase activity. Y1H and EMSA assays revealed that MdILR3 directly interacted with the promoters of MdNRT2.3/2.4 and MdNIA1. Furthermore, MdILR3 can directly bind to the promoter of MdSWEET12 and activate its expression, thereby regulating sucrose transport to provide energy for N uptake in roots. In summary, we provide physiological and molecular evidence suggesting that MdILR3 may positively regulate nitrate response by activating the expression of genes related to N uptake and sugar transport. Our findings suggest that genetic improvements in apple could enhance its ability to absorb and utilize N.