Abstract: The effects of nitrogen (N) application rate on the yield and greenhouse gas emissions (CH₄ and N₂O) of ratoon rice were investigated to provide a reference for the optimal N application rate for planting ratoon rice in the Taihu Lake region. From April to October 2022, a static chamber-gas chromatography method was used to observe the CH₄ and N₂O emission fluxes of ratoon rice under three different N fertilization rates FL1: 75 kg(N)·hm⁻², FL2: 125 kg(N)·hm⁻², FL3: 175 kg(N)·hm⁻² in Yixing, Jiangsu Province, while setting no fertilization treatment (FL0) as a control. The yield and its constituent factors were observed during the rice harvest. The results showed that the peak N₂O emission caused by bud-promoting fertilizer was the highest, and it showed a linear increasing trend with the increase of N fertilization rate; the total amount it caused accounted for 10.0%−50.7% of the entire growth period. Overall, the total (main reason+ratoon reason) N₂O emissions ranged from 1.30 to 8.69 kg(N)·hm⁻², with 6.94%−22.7% derived from ratoon rice; the N₂O emission factor during the ratoon season ranged from 0.38% to 1.71%. Seasonal cumulative CH₄ emissions ranged from 58.1 kg·hm⁻² to 78.7 kg·hm⁻², with 13.3%−23.8% in ratoon rice. Total CH₄ emissions were not significantly affected by an increase in N application rate. The total rice yield was 8.33–11.6 t·hm⁻², and the ratoon rice yield contributed 34.0%−46.1%. Compared to FL1, the ratoon season yields of FL2 and FL3 increased by 32.3% and 17.7%, respectively, which was related to an increase in effective panicle number by 27.2% and 13.5%, respectively. The greenhouse gas emission intensity during the entire growth period was 0.26−0.54 t(CO₂) e·t⁻¹, and compared with FL1, FL3 increased by 38.5%, and FL2 increased by 10.3%. Overall, both high yield and relatively low greenhouse gas emission intensity can be obtained by applying 125 kg(N)·hm⁻² in ratoon season. This N application rate is recommended for the storage of ratoon rice in Taihu Lake.