Abstract: To investigate the effects of annual nitrogen fertilizer management on crop yield and greenhouse gas emissions in a rice-wheat rotation system, ‘Shu mai 1963’ and ‘Indica three-line hybrid rice Chuankangyou 6308’ were used as test materials. Four annual nitrogen fertilizer management treatments were set up: annual N free (CK), 120 kg(N)·hm⁻² for wheat and 180 kg(N)·hm⁻² for rice (D₁), 150 kg(N)·hm⁻² for wheat and 150 kg(N)·hm⁻² for rice (D₂), and 180 kg(N)·hm⁻² for wheat and 120 kg(N)·hm⁻² for rice (D₃). The effects of these treatments on crop yield formation and greenhouse gas emissions in the rice-wheat rotation system were studied, and the relationships between annual yield formation, nitrogen use, and greenhouse gas emissions were explored. The results showed that annual nitrogen fertilizer management in the rice-wheat rotation system had significant effects on dry matter accumulation, nitrogen use, yield, and greenhouse gas emissions of wheat and rice at main growth stages. The wheat yield was the highest under the D₃ treatment. Compared with the D₁ and D₂ treatments for wheat, respectively, the number of effective panicles was significantly increased by 2.74% and 1.86% (P<0.05), respectively, and the number of grains per panicle was increased by 6.62% (P<0.05) and 2.38%, respectively. The rice yield was the highest under the D₁ treatment. Compared with the D₂ and D₃ treatments for rice, respectively, the number of effective panicles was increased by 1.65% and 5.12% (P<0.05), respectively, and the number of grains per panicle was significantly increased by 2.89% and 5.00% (P<0.05), Although the annual yield of the rice-wheat rotation system was the highest under the D₁ treatment, there was no significant difference compared with the D₂ treatment. The annual nitrogen physiological use efficiency was the highest under the D₂ treatment. In the N₂O emissions of the rice-wheat rotation system, wheat N₂O emissions account for 62.65%−72.41%; CH₄ emissions are dominated by rice CH₄ emissions, while wheat is in an overall absorption state. The annual GWP of the rice-wheat rotation system was the highest under the D₁ treatment, which was significantly increased by 7.31% and 15.27% compared with the D₂ and D₃ treatments, respectively (P<0.05), with the largest greenhouse gas emissions. Principal component analysis and correlation analysis showed that among the yield, nitrogen use, and greenhouse gas emission indicators, Number of effective panicles of wheat and dry matter accumulation had the strongest correlation with the three, for rice, the correlations with the three were mainly reflected in the number of grains per panicle and dry matter accumulation. Comprehensive evaluation showed that under the premise of maintaining the annual yield of the rice-wheat rotation system, the D₂ treatment reduced the annual greenhouse gas emissions and improved the annual nitrogen physiological use efficiency. This result can provide a theoretical and practical basis for the implementation of annual high-yield and efficient emission reduction cultivation techniques in the rice-wheat rotation area of Southwest China.