In order to fully realize the yield potential of good quality rice and the efficient utilization of water and nitrogen (N) resources, we explored the effects of water management (W), N application level (N) and application method (D) as well as their interaction on rice yield, grain structure and N use efficiency by a field experiment with the good quality hybrid rice Jingyou127 as material. The results showed that the yield of Jingyou127 was extremely significant effected by W, N and the interactions of W×N, W×D, N×D and W×N×D. The effect of D on yield was close to the significant level (P=0.050 5), the yield of Jingyou127 was highest when 75% N as base fertilizer and 25% as panicle fertilizer in wet-shallow alternate irrigation. W, N, D and their interactions had different effects on grain structure. Path analysis showed that the effective panicles and spikelets per panicle were the main factors of the yield. Except D and W×N,the other factors and their interactions had significant effects on N agronomic efficiency. Under the wet-shallow alternate irrigation, N agronomic efficiency was significantly lower than that under conventional irrigation, and it significantly decreased with the increase of N application level at postponing N application treatment, but little difference under conventional N application treatment, which had the opposite effect. Except D, the other factors and their interactions had significant effects on the partial factor productivity of applied N. Under the wet-sallow alternate irrigation, the partial factor productivity of applied N was significantly higher than that under conventional irrigation, and it significantly decreased with the increased N application level. Wet-shallow alternate irrigation, 100 kg/hm² N (75% as base fertilizer and 25% as panicle fertilizer) is the best model of water-nitrogen coupling management.