In order to further investigate the high water use efficiency mechanism under different water and nitrogen managements, theoretical analysis was combined with field experiments, and water use efficiency research on leaf scales was integrated through carbon isotope’s instruction on water use efficiency based on carbon isotopic factor effect during crop growth and development. The effects of different water and nitrogen managements on gas exchange parameters, instantaneous water use efficiency (WUEins), intrinsic water use efficiency (WUEint) and carbon isotope discrimination (Δ13C) were examined, and then the relationship between Δ13C in rice leaf with WUEins and WUEint at leaf scale was analyzed to further explain the water use process in crop leaf under different water and nitrogen managements. The result showed that the appropriate amount of nitrogen fertilizer could increase the stomatal conductance (Gs) of leaves of rice, promote the exchange of leaf cells with outside world, increase the net photosynthetic rate (Pn), and maintain high WUEint and WUEinsunder controlled irrigation. Excessive application of nitrogen would increase the sensitivity of rice to water deficit, so that Gs of rice leaves was reduced, which was not conducive to the efficient use of water at leaf scale. The leaf water use efficiency and yield were the highest when the nitrogen application rate was high at the heading stage, and WUEint, WUEins and WUEET of the same nitrogen treatment of controlled irrigation for rice were higher than those of flood irrigation, which played water saving and high yield effect. The statistical analysis result indicated that leaf Δ13C showed a negative relationship with WUEint,WUEins and WUEET respectively at heading stage under different water and nitrogen managements. Leaf Δ13C showed a better indicating capacity on WUEint than that on WUEins. Furthermore, the correlation between leaf Δ13C and WUEins, WUEint under controlled irrigation was more significant than that under flooding irrigation;the leaf Δ13C values can well characterize rice WUEET during the period of booting and heading. In conclusion, using rice leaf Δ13C values to indicate water use efficiency at leaf levels had a certain feasibility under different water and nitrogen managements.