This study intended to investigate the greenhouse gases emission from Japan single cropping paddy fields after 75-year continuous application of ammonium sulfate, composted rice straw with soybean cake, and fresh clover, as well as the environmental impact of the emission. During this long period, field management remained constant in terms of rice cultivation density, irrigation, and equivalent net N fertilization. No significant differences were observed in N2O emission among the fertilization treatments, but the CH4 emission differed significantly between organic amendment and ammonium sulfate application, indicating that long-term organic fertilization didn' t increase N2O emission but promoted CH4 emission. The cumulative global warming potential (GWP) of the CH4 and NO2O from the paddy ecosystem was the greatest (310.7 g CO2e x m(-2)) under fresh clover application, followed by composted rice straw plus soybean cake addition (151 g CO2e x m(-2)), and the least (60.6 g CO2e x m(-2)) under ammonium sulfate application. This study showed that for paddy system, it was CH4 instead of N2O the major factor affecting global warming, and thereby, to control and reduce the CH4 emission from paddy system would be the core in mitigating greenhouse gases emission from paddy field. Long-term consecutive application of composted rice straw plus soybean cake could increase soil organic matter, improve soil fertility, promote rice high-yielding, and as well, mitigate CH4 emission, being the recommendable paddy rice production mode in practice.