Nitrogen (N) allocation in leaves affects plant photosynthesis-N relationship and adaptation to environmental fluctuations. To reveal the role of leaf N allocation in water deficit stress acclimation in rice, the plants were grown in infertile soil supplying with low N (0.05 g N·kg⁻¹ soil) and high N (0.2 g N·kg⁻¹ soil), and then imposed to water deficit stress (∼75% relative soil water content). We found that the proportion of leaf N allocated in the photosynthetic apparatus was significantly positive correlated with photosynthetic N-use efficiency (PNUE), and that N allocation in the carboxylation system and bioenergetics were the primary two limiting factors of PNUE under the conditions of high N and water deficit stress. PNUE was not significantly affected by water stress in low N condition, but markedly reduced in high N condition. Under low N condition, plants reduced N allocation in the light-harvesting system and increased soluble protein and free amino acids, or reduced N allocation in the cell wall to maintain PNUE under water deficit stress. Under high N, however, plants decreased N allocation in bioenergetics or carboxylation, but increased N allocation in non-photosynthetic components during water stress. Our results reveal that the coordination of leaf N allocation between photosynthetic and non-photosynthetic apparatus, and among the components of the photosynthetic apparatus is important for the trade-off between PNUE and the acclimation of water deficit stress in rice.