Field experiments were conducted in 2005 and 2006 to investigate the impacts of alternative rice cultivation systems on grain yield, water productivity, N uptake and N use efficiency (ANUE, agronomic N use efficiency; PFP, partial factor productivity of applied N). The trials compared the practices used with the system of rice intensification (SRI) and traditional flooding (TF). The effects of different N application rates (0, 80, 160 and 240 kg ha−1) and of N rates interacting with the cultivation system were also evaluated. Resulting grain yields with SRI ranged from 5.6 to 7.3 t ha−1, and from 4.1 to 6.4 t ha−1 under TF management. On average, grain yields under SRI were 21% higher in 2005 and 22% higher in 2006 than with TF. Compared with TF, SRI plots had higher harvest index across four fertilizer N rates in both years. However, there was no significance difference in above-ground biomass between two cultivation systems in either year. ANUE was increased significantly under SRI at 80 kg N ha−1 compared with TF, while at higher N application rates, ANUE with SRI was significantly lower than TF. Compared with TF, PFP under SRI was higher across all four N rates in both years, although the difference at 240 kg N ha−1 was not significant. As N rate increased, the ANUE and PFP under both SRI and TF significantly decreased. Reduction in irrigation water use with SRI was 40% in 2005 and 47% in 2006, and water use efficiency, both total and from irrigation, were significantly increased compared to TF. With both SRI and TF, the highest N application was associated with decreases in grain yield, N use efficiency and water use efficiency. This is an important finding given current debates whether N application rates in China are above the optimum, especially considering consequences for soil and water resources. Cultivation system, N rates and their interactions all produced significant differences in this study. Results confirmed that optimizing fertilizer N application rates under SRI is important to increase yield, N use efficiency and water use efficiency.