The use of polymer-coated urea (PCU) can improve nitrogen use efficiency (NUE), compared to the application of rapid-release urea (RU). However, the effect of PCU-based nitrogen management on grain yield and the NUE of rice and its underlying mechanism remain unclear. A japonica rice cultivar Jinxiangyu 1 was grown in the field with four treatments including N omission (0N), split application of RU (Control), one-time application of 100% PCU (T1), and one-time application of 70% PCU + 30% RU (T2). Results showed that, compared to the control, the grain yield was significantly increased in the T2 treatment, while it was comparable in the T1 treatment. This was mainly due to increased total spikelets in the T2 treatment. Root oxidation activity (ROA) and root zeatin (Z) + zeatin riboside (ZR) content during booting were the distinct advantages of the T2 treatment, compared to either the control or T1 treatment, exhibiting significant or highly significant correlations with leaf photosynthesis. This process contributed significantly to total spikelets and total N uptake. Additionally, the T2 treatment absorbed more N than the control without reducing the internal N use efficiency (IEN), primarily due to its unchanged harvest index (HI) driven by comparable non-structural carbohydrate remobilization. In conclusion, combining PCU with RU can enhance the coordination of root and shoot traits during booting while maintaining a competitive HI at maturity, thereby significantly improving grain yield and achieving a balance in N uptake and utilization.