An understanding of the leaf and root traits associated with high nitrogen (N) absorption and utilization is very important in the development of N-efficient varieties in crop breeding programs. However, in rice, the relations between these traits and nitrogen use efficiencies (NUEs) have yet to be identified. Therefore, the responses of leaf and root traits and yields of the three main japonica rice cultivars in northern China were examined at a range of N application rates. The rice cultivars, Shennong 265 (SN265), Tiejing 11 (TJ11), and Fengjing (FJ), were grown in the field at six N rates (0, 60, 120, 180, 240, and 300 kg ha−1) applied during two growing seasons (2018 and 2019). With the increase in N rate, the grain yield of SN265 and TJ11 increased, whereas the grain yield of FJ first increased and then decreased. The grain yield of FJ was higher than that of SN265 and TJ11 at lower N rates, whereas the grain yields of SN265 and TJ11 were higher than that of FJ at higher N rates. The NUEs decreased with the increase in N rates. At lower N rates, the ability of rice to obtain N was the main limitation on rice yield, but with the increase in N rates, the limitation on yield due to N absorption capacity gradually weakened. However, at higher N rates, rice yields were restricted by the ability to utilize N. Compared with TJ11 or FJ, SN265 had higher N utilization capacity primarily because of its higher Rubisco activity, NR activity, GS activity, and ROA. Compared with SN265 or TJ11, FJ had a higher N absorption capacity that was attributed to its larger root architecture, which might have also been one of the reasons for lower N utilization. Therefore, by improving N absorption and utilization-related leaf and root traits, high yields and NUEs can be achieved in rice production at different N application rates.