Abstract: To investigate the effects of annual nitrogen (N) fertilizer management on crop yield and greenhouse gas emissions in a rice-wheat rotation system, ‘Shumai 1963’ and ‘Indica three-line hybrid rice Chuankangyou 6308’ were used as test materials. Four annual N fertilizer management treatments were established: 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 and greenhouse gas emissions in a rice-wheat rotation system were studied, and the relationships between annual yield, N use, and greenhouse gas emissions were explored. The results showed that annual N fertilizer management in the rice-wheat rotation system had significant effects on dry matter accumulation, N use, yield, and greenhouse gas emissions of wheat and rice at the primary growth stages. Compared with the D₁ and D₂ treatments for wheat, wheat yield under the D₃ treatment significantly increased by 10.82% and 5.29%, respectively, the number of effective panicles under the D₃ treatment significantly increased by 2.74% and 1.86% (P<0.05), respectively, and the number of grains per panicle under the D₃ treatment increased by 6.62% (P<0.05) and 2.38%, respectively. Compared with the D₂ and D₃ treatments for rice, rice yield under the D₁ treatment significantly increased by 5.93% and 15.72%, respectively, the number of effective panicles under the D₁ treatment increased by 1.65% and 5.12% (P<0.05), respectively, and the number of grains per panicle under the D₁ treatment significantly increased by 2.89% and 5.00% (P<0.05), respectively. Although the annual yield of the rice-wheat rotation system was highest under the D₁ treatment, there was no significant difference compared with the D₂ treatment. The annual N physiological use efficiency was highest under the D₂ treatment. Regarding to the N₂O cumulative emissions from rice-wheat rotation system, N₂O cumulative emissions from wheat season accounted for 62.65%−72.41%; CH₄ cumulative emissions were dominated by CH₄ cumulative emissions from rice season, whereas CH₄ emissions from wheat season was in an overall absorption state. The annual GWP of the rice-wheat rotation system was highest under the D₁ treatment, which significantly increased by 7.31% and 15.27% (P<0.05) compared to the D₂ and D₃ treatments, respectively. Principal component and correlation analyses showed that, in terms of yield, N use, and greenhouse gases emission indicators, the number of effective wheat panicles and dry matter accumulation had the strongest correlations with these three indicators, whereas for rice, the correlations were mainly reflected in the number of grains per panicle and dry matter accumulation. A 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 annual N physiological use efficiency. These results can provide a theoretical and practical basis for the implementation of annual high-yield and efficient emissions reduction cultivation techniques in the rice-wheat rotation region in Southwest China.