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We sought to explore the role of postanthesis carbon and nitrogen (C-N) metabolism of hybrid rice in increasing yield and nitrogen utilization efficiency (NUE). We used the ¹³C and ¹⁵N dual-isotope tracer method and physiological/biochemical analysis and established different irrigation and nitrogen fertilization (W-N) regimes to investigate the relationship of C-N metabolism characteristics, yield, and NUE. The results showed that W-N regimes had significant effects on postanthesis absorption and translocation of N and photosynthate, yield and NUE. Aerobic irrigation combined with the N fertilization regime 30% base, 30% tillering, 40% booting was the best W-N coupling regime for rice yield and NUE increase. The regime enhanced flag leaf photosynthesis rate and the activities of ribulose 1,5-diphosphate carboxylase/oxygenase (RuBPCase), glutamine synthetase (GS), and other key enzymes of C-N metabolism, and improved the total accumulations of photoassimilates (0.97–21.57 mg ¹³C plant⁻¹) and N (1.55–23.36 mg ¹⁵N plant⁻¹), respectively. Correlation analysis showed that, under the W-N interaction, C-N metabolism enzymes promoted the positive synergistic effect between ¹³C and ¹⁵N accumulation in panicles (r = 0.825). In addition, the change in C/N ratio can be used as an indicator of the simultaneous improvement in yield and NUE in hybrid rice.