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Nitrogen (N) is an essential macronutrient that limits agricultural productivity; however, excessive N fertilizers are still used, especially in China. Improving crop N use efficiency (NUE) is an effective measure to reduce environmental pollution and is a primary direction in agricultural crop improvement. Although the physiological and molecular mechanisms for uncovering differences in NUE have become increasingly important, only a few crops have been studied to date. Two proso millet (Panicum miliaceum L.) cultivars with contrasting NUE, the low–N–tolerant cultivar (T184) and the low–N–sensitive cultivar (S111), were used to explore physiological as well as comparative transcriptomic mechanisms for earning high NUE in field and hydroponic experiments. The results showed that T184 had higher N uptake and utilization efficiencies and better photosynthetic capacity than S111 in field trials, as measured by increased chlorophyll content and net photosynthetic rate. Meanwhile, improved NUE and yield of T184 were observed compared with S111 under different N regimes. In hydroponic experiments, T184 had higher photosynthetic capacities in leaves and higher N metabolism enzyme activities in leaves and roots than S111, despite the photosynthetic and physiological parameters exhibited decreasing tendency to N deficiency in both T184 and S111. Furthermore, transcriptomic analysis revealed that T184 had less differentially expressed genes (DEGs) than S111. Many genes involved in photosynthesis and N uptake and assimilation were implicated in conferring NUE. Four nitrate transporter genes and eight photosynthetic genes were higher in T184 than in S111 under low and recovery N conditions and were strongly associated with NUE. These results revealed that greater N uptake and utilization efficiencies, accelerated N assimilation and translocation, and enhanced photosynthetic activity confer higher NUE in proso millet. • The low N–tolerant proso millet had increased N uptake, N utilization efficiency (NUE), and grain yield. • Higher photosynthetic capacity and physiological metabolism of the low–N–tolerant proso millet were observed. • Identify photosynthesis candidate genes could facilitate breeding for enhanced NUE. • High N uptake and utilization efficiencies, maintained photosynthesis, and N transport resulted in a higher NUE. [ABSTRACT FROM AUTHOR]