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Paddy rice cultivation is an important source of global anthropogenic methane emissions. Drainage the flooded soils can reduce methane substantially, but N2O emission occur concurrently, which would offset the reduction of methane emission. It remains unclear how mid-season drainage affects the global warming potential (GWP) of CH4 and N2O emissions. In this study, a meta-analysis was conducted to investigate the effect of mid-season drainage on GWP and the factors that control the response of GWP to mid-season drainage. Results showed that mid-season drainage decreased CH4 emission by 52% while increased N2O emission by 242%. The GWP under mid-season drainage decreased by 47% compared to continuously flooding. The yield-scaled GWP under mid-season drainage decreased by 48%. Mid-season drainage had no effect on rice grain yield. Although soil drainage times and organic matter amendment are important factors affecting CH4 and N2O emissions in rice paddy field, the study showed that neither of them had effect on the response of GWP to mid-season drainage. The reduction rate of the GWP under mid-season drainage increased when N fertilization application rate increases from 50 kg ha(-1) to > 200 kg ha(-1). This study demonstrated that CH4 is still a dominant greenhouse gas in rice paddies under water management with mid-season drainage. Nitrogen fertilization is an important factor that regulates the response of GWP to mid-season drainage. High nitrogen fertilization rate would decrease the overall emission of CH4 and N2O under mid-season drainage. However, increasing drainage times or applying organic fertilizer under mid-season does not change the overall emission rate of CH4 and N2O.