Soil water potential and fertilizer nutrients are the two main factors affecting rice growth and development. A soil‐grown experiment was conducted using mid‐season japonica rice cultivar Xudao 3 with three different nitrogen (N) fertilization rates: (i) none, (ii) moderate nitrogen (240 kg ha–1), and (iii) high nitrogen (360 kg ha–1) and three irrigation regimes: (i) submerged irrigation (0 kPa), (ii) alternate wetting and moderate drying (–20 kPa), and (iii) alternate wetting and severe drying (–40 kPa). In the same N level, root length, root dry weight, root activity (represented by root‐bleeding sap), net photosynthetic rates at main growth stages, and ATPase activity during the grain‐filling stage are higher under the treatment of alternate wetting and moderate drying, when compared with those of submerged irrigation. Meanwhile, non‐structural carbohydrate (NSC) remobilization and shoot dry accumulation are also increased from heading to maturity, which contribute to higher grain yield and higher nitrogen‐use efficiency. In the same irrigation regime, root‐bleeding sap, NSC remobilization, and ATPase are increased significantly under the moderate‐N treatment compared with those of the high‐N treatment, which contribute to higher nitrogen‐use efficiency. However, no significant difference exists in grain yield and crop growth rate. These results indicate that the coordinated relationship between the root and shoot, especially increased root length, enhanced root‐bleeding sap, increased NSC remobilization, enhanced shoot dry accumulation, and ATPase activity during the grain‐filling stage, can promote rice yield and nitrogen‐use efficiency by using the appropriate nitrogen application and alternate wetting and moderate drying. Core Ideas Root and shoot traits were significantly different in response to irrigation regime and nitrogen level treatment. Alternated wetting/moderate drying interacted with moderate N to coordinate the development of root and shoot. Deeper roots increased root‐bleeding sap, NSC remobilization from stems to grain, and activity of grain sink. Greater root length (via root‐shoot relationships) contribute to increased yield and enhanced N‐use efficiency. Alternated wetting/drying irrigation with moderate N promotes grain filling and increased yield and N‐use.