To investigate the effects of water-nitrogen management on nitrogen(N), phosphorus(P) and potassium(K) uptake and translocation of stem-sheath and leaf of rice and their relationships with grain yield, we applied two water management and three nitrogen management on the wheat stubble hybrid indica rice cultivar F You 498.The two water management was submerged irrigation and alternating dry-wet irrigation and the nitrogen managements was 150 kg/hm2 of nitrogen application rates with three nitrogen management—the ratio of the basal fertilizer, tillering fertilizer and panicle fertilizer were 4∶4∶2(T1), 3∶3∶4(T2) and 2∶2∶6(T3), respectively—as well as the control without nitrogen application. Compared with submerged irrigation, alternating dry-wet irrigation was in favor of improving N and K accumulation in stem-sheath and leaf of rice at the heading stage and maturity stage, and improving K accumulation in panicle and total K accumulation of plants at the maturity stage. The P and K accumulation in stem-sheath, leaf and plants showed increased first and then decreased with postponing N fertilizer. However, the P accumulation could be improved in submerged irrigation. Meanwhile, the N, P, K accumulation in stem-sheath and leaf of rice were increased with postponing N fertilizer in submerged irrigation. The alternating dry-wet irrigation could significantly enhance the N and K translocation amount and translocation conversion rate of rice, and improve spikelet number per panicle, seed-setting rate, 1 000-grain weight and grain yield. With the nitrogen managements, the grain yield of rice in T2 treatment could be increased by 9.09%, 6.48% (submerged irrigation) and 11.24%, 11.05% (alternating dry-wet irrigation) than T1 and T3 by suitably postponing N application. The higher grain yield of rice could be achieved through the ration of basal fertilizer, tillering fertilizer and panicle fertilizer was 3∶3∶4 combined with 150 kg/hm2 of nitrogen application rates in alternating dry-wet irrigation.