AbstractIncreasing the application of nitrogen fertilizer is the main approach to increase rice production, but it also brings problems of environmental pollution and increases agricultural production costs. Cultivating high‐yielding and high nitrogen use efficiency (NUE) rice varieties is an important approach to solving this problem. The rice varieties carrying dep1 (dense and erect panicle 1) have both high grain yield and high NUE. However, their plant traits have not been fully explored. In this study, two rice near‐isogenic lines carrying dep1 (NIL‐DEP1 and NIL‐dep1) were grown in paddy fields under 0, 120 and 270 kg N ha−1. We analyzed agronomic traits of panicle type, plant type, leaves and roots, and physiological traits of vascular bundles, photosynthetic rate and carbon and nitrogen transport. The results showed that the NIL‐dep1 exhibited higher grain yield and NUE than NIL‐DEP1, mainly due to the higher spikelet number per panicle, grain filling percentage and dry matter production. Compared with NIL‐DEP1, NIL‐dep1 had improved flag leaf morpho–physiological traits, including erect flag leaves, greater leaf thickness and specific leaf weight, higher root dry weight, root length, root volume and root surface area, and a better canopy structure, as reflected by a lower light interception percent and canopy extinction coefficient, leading to better photosynthetic performance and dry matter production. In addition, NIL‐dep1 exhibited better vascular bundle traits of peduncle and enhanced dry matter, stem carbon and nitrogen translocation during grain filling. In conclusion, NIL‐dep1 had high grain yield and NUE by improved agronomic and physiological traits and increasing carbon and nitrogen translocation during grain filling. These traits mentioned above could be used to select and breed high grain yield with high NUE rice varieties.