Slow/controlled release nitrogen fertilizers, providing a gradual nutrient supply for a long time period, improve nitrogen fertilizer use efficiency and reduce nitrogen leaching losses. However, the effectiveness of slow/controlled release nitrogen fertilizers will be strongly affected by the environmental conditions, especially by water conditions, in the planting region. Alternate wetting and drying (AWD) irrigation has been widely adopted to replace continuous flooding irrigation for saving water and increasing water use efficiency (WUE) in irrigated rice(Oryza sativa L.) systems. However, little attention has been paid to the performance of slow/controlled release nitrogen fertilizers and its mechanism of realizing high yield under different water managements. A field experiment was conducted to investigate the effects of slow/controlled release nitrogen fertilizers on biomass and nitrogen accumulation, translocation and distribution in rice, together with the mechanism, with a split-split design in 2012 and 2013. The main plot treatment was different water managements, including controlled irrigation (W1), alternate wetting and drying irrigation (W2) and flooding irrigation (W3), and the subplot treatment contained urea single basal application (F1), urea applying with ratio of base : tillering : earring = 5:3:2 (F2), sulfur coated N fertilizer single basal application (F3) and resin coated N fertilizer single basal application (F4). Results showed that there was a significant interactive effect between water management and slow/controlled release nitrogen fertilizers application on biomass, nitrogen accumulation, translocation and distribution and rice yield in the main growth period. Moreover, there existed significantly positive correlations between yield component factors and nitrogen increasing in panicle, nitrogen translocation and distribution at heading stage. In addition, AWD and slow/controlled release nitrogen fertilizers had a significant interactive effect, enhancing biomass, nitrogen accumulation and yield in rice. Nitrogen use efficiency, partial factor productivity of applied nitrogen, nitrogen agronomic efficiency and yield increased by 42%–53%, 6%–23%, 26%–71%, and 8%–19% respectively in F3, as compared with F1 and F2 treatments. Different types of nitrogen fertilizer and water condition affected rice yield mainly through affecting available spike number and grain number per spike. The application of slow/controlled release nitrogen fertilizers enhanced nitrogen use efficiency and maintained heavy and adequate panicles under controlled irrigation condition. Under alternate wetting and drying irrigation, the beneficial effect of using slow/controlled release nitrogen fertilizers was attributed to better nitrogen accumulation capacity and more coordinated nitrogen distribution in rice plant, which results from slowing the release of nitrogen into the soil relative to regular fertilizer and water conditions, and improving synchronization with crop N requirements during crop growth. Under flooding irrigation condition, slow/controlled release nitrogen fertilizers reduced ineffective tillering and nitrogen losses of leaching and penetrating, resulting in high earbearing tiller percentage. In conclusion, applying slow/controlled release nitrogen fertilizers under alternate wetting and drying irrigation condition can enhance nitrogen use efficiency and realize high yield.