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A 2-year field study was conducted in a double rice cropping system in southern China to examine the effect of fertilization on CH4, N2O and CO2 fluxes using static opaque chambers and gas chromatographs. Two treatments were set up including conventional fertilization with a rate of 358 kg N/ha per year in forms of compound fertilizer and urea, and a control with no fertilizer application. The results indicated that fertilization did not have a significant effect on CH4 fluxes and led to a significantly higher cumulative N2O emission in the two years of observation period. Fertilization promoted CO2 fluxes by increasing the autotrophic respiration instead of heterotrophic respiration. By combining the global warming impact of CH4, N2O and CO2, it was found that fertilization increased the area-scaled but not the yield-scaled global warming impact. These results indicated that, according to the current amount of nitrogen applied, fertilization may increase the global warming effect of paddy fields in this region. However, the appropriate dose of nitrogen fertilizer application is still a reasonable agricultural management due to the comprehensive consideration of production and environmental impacts.