Abstract: Soil moisture and nitrogen (N) nutrient are the principal factors affecting rice production. Elucidation of their influences and coupling effects on grain yield of rice (Oryza sativa L.) would have great significance for high yielding and high efficiency of rice. As early as in 1911, Montgomery had began to study the effects of soil fertility on water consumption of maize in Mabraka, and Painten and Leamer noted that higher yield was obtained by applying more fertilizer under the condition of higher soil water potential in 1953. Domestic and foreign scholars have conducted extensive researches on the interaction of water and fertilizer. The existed researches focused on crop growth development, photosynthetic characteristics, yield and quality formation, nutrient and water use efficiency and other aspects of the studies, but most researches focused on the ground, few papers for the root characteristics, and the conclusions were not consistent. The purposes of this study were to investigate the effects of water and N coupling on root morphology and physiology, grain yield and N fertilizer use efficiency. A mid-season japonica rice cultivar of Xudao 3 was planted. Three treatments of different N levels, i.e. no N fertilizer application, normal N (MN, 240 kg/km2) and high N (HN, 360 kg/hm2) and 3 irrigation regimes, i.e. submerged irrigation (0 kPa), alternate wetting and moderate drying (-20 kPa) and alternate wetting and severe drying (-40 kPa) were conducted. The results showed that there was a significant interaction between irrigation regimes and N applications, while not significant between the years for the main indices. In the same N condition, grain yield increased under the mild water stress, yet decreased significantly under the condition of alternate wetting and severe drying, an average reduction of 29.8%. When compared with no N fertilizer, rice yield of MN and HN treatment improved by from 54.0% to 60.6% (submerged irrigation), from 57.0% to 66.4% (-20 kPa) and from 33.0% to 61.0% (-40 kPa), and the result indicated that the application of N fertilizer could enhance rice yield significantly. Compared with the MN, grain yield under the condition of HN treatment was reduced, but the difference was not significant, except while water stress was severe, the yield of HN decreased significantly (P<0.05). High N fertilizer application had aggravated the soil drought, and reduced the effect of fertilizer regulation. The grain yield was the highest under the interaction of MN and mild water stress through the analysis of coupling effect of water and N, and the reason was it improved the filled grain rate and the 1000-grain weight when compared with other treatments. Under mild drying condition, root length, root dry weight, root activity, total root absorbing area, activity absorbing area and N metabolism enzyme activity at main growth stages were increased, but root-shoot ratio was decreased after panicle initiation stage. Mild water stress and MN enhanced rice yield and N use efficiency, being the best mode in this paper referred as the water-nitrogen coupling management mode．The opposite result was observed under the condition of alternate wetting and severe drying. Correlation analysis showed that grain yield was positively correlated to all the above morphological and physiological indices at main growth stages with the exception of negative correlation of the root-shoot ratio at the stage of heading．A negative correlation was observed between the N agronomy efficiency and the root dry weight, dry weight density, root-shoot ratio, while there was significant or extremely significant positive correlation between root active absorbing area, root activity at heading stage and N agronomy efficiency. These results suggest a good root morphology can increase root activity and N metabolism enzyme activity through the regulation of water and N, and will be much more beneficial to increasing grain yield and N use efficiency in rice production.