Sub-low temperatures in spring often cause stress to the apple root system, inhibiting nitrogen uptake due to lower soil temperatures and reducing root function. Despite research on the function of sugar in regulating plant nitrogen metabolism, the mechanism through which sucrose regulates nitrogen uptake in apple roots at sub-low root-zone temperatures remains unknown. In this study, 1% sucrose was applied at sub-low temperatures in the root zone of Malus baccata Borkh, a widely used apple rootstock, to elucidate the physiological, transcriptional, and metabolic mechanisms of plant nitrogen uptake regulation by sugar. The results showed that adding sucrose promoted root development, accelerated carbon metabolism, provided more carbon skeletons and energy for nitrogen assimilation, and increased the activity of enzymes related to nitrogen metabolism, facilitating nitrogen uptake and utilization. This, in turn, increased the photosynthetic capacity of leaves and facilitated plant growth and development. In contrast, the sub-low root-zone temperature treatment significantly inhibited root development, nitrogen uptake, photosynthesis rate, and plant growth and development. The majority of the genes encoding enzymes associated with carbon and nitrogen metabolism (amylase, sucrose synthase, ATP-dependent 6-phosphofructokinase, pyruvate kinase, nitrate transporter, glutamine synthase, and glutamate dehydrogenase) were upregulated upon exposure to sucrose, as confirmed by transcriptomic data. Furthermore, the metabolomic results suggested that sucrose might enhance nitrogen uptake by modulating flavonoid metabolism. Taken together, these results provide new insights into the role of sucrose in modulating root system nitrogen uptake in the root zone at sub-low temperatures.