Organic amendment often affects both crop yield and greenhouse gas (GHG) emission. Yet the impact of organic amendment on yield gains and GHG emissions is still unclear, particularly in long-term wheat cropping system. Based on a 30-year experiment, the impact of organic amendments (i.e. straw and manure) on soil properties, wheat yield and yield stability, N2O and CH4 emissions, and net ecosystem economic budget (NEEB) were investigated. The treatments were: chemical NPK fertilizer (NPK), chemical NPK plus low amount of wheat straw (NPKLS), chemical NPK plus high amount of wheat straw (NPKHS), chemical NPK plus pig manure (NPKPM), chemical NPK plus cattle manure (NPKCM), and a control with no fertilizer applied (CK). The long-term straw and manure amendments enhanced wheat yield by 6.4% and 9.9%, respectively, as well as yield stability. Meanwhile, they stimulated N2O emissions by 19.9% and 52.2% respectively, without significant effect on CH4 emissions, compared to the chemical NPK fertilizer treatment (NPK). The results of structural equation model showed that soil properties tested explained 76% of the variations observed in N2O emissions, which were directly affected by soil nitrification capacity, pH and denitrification capacity. Although straw and manure amendments increased the total GHG emissions investigated by 19.2% and 51.1% respectively, they showed insignificant effects on the greenhouse gas intensity (GHGI), and increased NEEB by 6.4% and 9.7%, respectively, compared to the NPK treatment. This indicates that the benefits arising from crop yield improvement through the use of organic amendments can cover the carbon fees caused by increased GHG emissions. Our findings suggest that organic amendment can be an effective strategy to simultaneously increase wheat yield while mitigating greenhouse gas emissions from the perspective of carbon fees.