Abstract: To explore the quantitative relationship between CH₄ and N₂O emissions with nitrogen fertilizer application rates in the rice-wheat rotation system in Jiangsu Province and to determine the optimal fertilization scheme, a multi-level quantitative nitrogen application experiment was conducted to accurately estimate the relationship between N₂O and CH₄ emissions with nitrogen application in the rice-wheat rotation system. A carbon footprint (CF) and net ecosystem economic benefits (NEEB) model for the rice-wheat rotation system was constructed. Based on this model, an optimized fertilization scheme was put forward, with the objective of providing theoretical support for measures to reduce emissions. A field experiment was carried out during the wheat and rice seasons between November 2022 and October 2023. The wheat season test was conducted with six nitrogen level treatments, specifically N0 (0 kg·hm^-2), N180 (180 kg·hm^-2), N240 (240 kg·hm^-2), N270 (270 kg·hm^-2), N300 (300 kg·hm^-2) and N360 (360 kg·hm^-2). The rice season test was conducted with five nitrogen level treatments, specifically N0 (0 kg·hm^-2), N180 (180 kg·hm^-2), N240 (240 kg·hm^-2), N300 (300 kg·hm^-2) and N360 (360 kg·hm^-2). The same nitrogen level was applied in the same experimental plot for rotation. Continuous monitoring of CH₄ and N₂O emissions in agricultural fields was conducted using static closed chamber/GC technique, with a comprehensive analysis of greenhouse gas emissions intensity based on rice-wheat yield and global warming potential. The results indicate that the N₂O emissions from the rice-wheat rotation system increased significantly with the increase of nitrogen application, and an exponential relationship was observed between N₂O emissions and nitrogen application. CH₄ emissions exhibited a pattern of initial decrease followed by an increase with rising nitrogen fertilizer application, and the most suitable equation for the methane-nitrogen relationship was found to be cubic function of one variable, which indicates that an appropriate nitrogen application rate can reduce CH₄ emissions. Throughout the rice-wheat rotation cycle, as nitrogen application increased, the contribution rate of N₂O to GWP gradually rose, while the contribution rate of CH₄ further declined. CH₄ emissions during the rice season consistently played a dominant role in GWP contribution. Therefore, when studying greenhouse gas emission reduction in a rice-wheat rotation system, it is essential to focus on CH₄ emissions during the rice season. The dominance of CH₄ emissions in the rice season on GWP was consistent across all nitrogen fertilizer treatments. Therefore, when studying greenhouse gas emission reduction in a rice-wheat rotation system, it is essential to focus on CH₄ emissions during the rice season. Synergizing the net ecosystem economic benefits and carbon emissions, a nitrogen application rate ranging from 267 to 283 kg·hm^-2 is the optimal fertilization scheme.