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Controlling agricultural greenhouse gas emissions, such as N 2 O, is important in mitigating global climate warming. Through monitoring the dynamics of N 2 O emission fluxes, we investigated the effect of organic nitrogen (N) substitution of synthetic N on N 2 O emissions and the yield of winter wheat and summer maize in the Guanzhong Plain of Shaanxi Province, China. The study involved six treatments, consisting of no fertilizer (CK), synthetic N, phosphorus (P), and potassium (K) fertilizers alone (NPK), 75% NPK+25% organic N through manure (25%M), 50% NPK+50% organic N (50%M), 25% NPK+75% organic N (75%M), 100% organic N (100%M). The results showed that the peak value of the N 2 O emission flux appeared after fertilization, rainfall, and irrigation. In the wheat season, the emission flux of N 2 O varied from -1.33 to 144.2 μg·(m 2 ·h) -1 , with the highest peak value in the NPK treatment. In the maize season, the emission flux of N 2 O varied from 88.2 to 1800.1 μg·(m 2 ·h) -1 , and the 50%M treatment showed the highest peak value. The range in the total amount of N 2 O emissions from the different treatments in the wheat-maize rotation system was 429.8-2632.1 g·hm -2 , and the amount for the treatments decreased in order as follows:50%M > 25%M > NPK > 75%M > 100%M > CK. The yields of wheat, maize, or wheat plus maize were significantly higher in the fertilized treatments compared to the CK. Organic substitution treatments significantly increased wheat yield by 26.1% to 50.0% relative to the NPK treatment. While the maize yield in 50%M and 75%M treatments was similar to that in the NPK treatment, the 25%M and 100%M treatments showed significantly lower yields than with the NPK treatment. The total yield of wheat plus maize varied from 9166 to 17496 kg·hm -2 , of which total yield was significantly higher with 50%M and 75%M compared to NPK. Overall, the 75%M treatment is the best measure to guarantee crop yield and to reduce N 2 O emissions in the wheat-maize rotation system based on a one year study in the Guanzhong plain of Shaanxi Province.