The incorporation of straw residues into fields and the application of nitrogen fertilizers represent two primary avenues for the supplementation of carbon and nitrogen elements in agricultural ecosystems. These practices play crucial roles in regulating greenhouse gas emissions, specifically methane (CH₄) and nitrous oxide (N₂O), as well as influencing rice crop yields. Previous research has predominantly focused on examining the individual im4 and N₂O emissions remain insufficiently elucidated. Simultaneously, there exists a dearth of in-depth investigations into the judicious application of nitrogen fertilizers under condition of straw incorporation. This study, based on multi-year in-field experiments in rice paddies, implemented three nitrogen fertilizer treatments (0, 180, and 360 kg N/hm²) and three straw incorporation treatments (0, 2.25, and3.75 t/hm²). Results revealed a positive correlation between the increased levels of straw incorporation and elevated seasonal cumulative CH₄ emissions, with no statistically significant positive correlation observed with nitrogen fertilizer levels. Conversely, the seasonal cumulative N₂O emissions demonstrated an increase commensurate with elevated nitrogen application levels, lacking a statistically significant positive correlation with straw incorporation levels. The impact of returning straw to the field on yield was uncertain, with the lowest yield observed in S0N0 treatment over two years. The lowest yields in 2021 and 2022 were 5740.64 and 4903.75 kg/hm², respectively. The highest production in 2021 and 2022 occurred in the treatments of S0N2 and S2N2, with 10938.48 and 10384.83 kg/hm², respectively. In the case of low straw incorporation, the carbon footprint (CF) of 251 kg N/hm² corresponded to the lowest carbon footprint, 1.01 kg C/kg; In terms of net ecosystem economic benefits (NEEB), the highest ecological and economic benefit was corresponding to the nitrogen application rate of 294 kg N/hm², which was 11778.15 CNY/hm². To optimize the ecological economic benefits and reduce carbon emissions under condition of low straw incorporation, the study recommended nitrogen application rate ranging from 251-294 kg N/hm² as the optimal fertilization scheme. The research results provide theoretical foundations for guiding mitigation strategies related to greenhouse gas emission in rice paddy fields, achieving carbon neutrality in paddy fields and farmland management, and informing agronomic practices for attaining high and stable rice yields with low-carbon production.