This study provides a complete account of global warming potential (GWP) and greenhouse gas intensity (GHGI) in relation to a long-term water management experiment in Chinese double-rice cropping systems. The three strategies of water management comprised continuous (year-round) flooding (CF), flooding during the rice season but with drainage during the midseason and harvest time (F-D-F), and irrigation only for flooding during transplanting and the tillering stage (F-RF). The CH4 and N2O fluxes were measured with the static chamber method. Soil organic carbon (SOC) sequestration rates were estimated based on the changes in the carbon stocks during 1998–2014. Longer periods of soil flooding led to increased CH4 emissions, reduced N2O emissions, and enhanced SOC sequestration. The net GWPs were 22,497, 8,895, and 1,646 kg CO2-equivalent ha−1 yr−1 for the CF, F-D-F, and F-RF, respectively. The annual rice grain yields were comparable between the F-D-F and CF, but were reduced significantly (by 13%) in the F-RF. The GHGIs were 2.07, 0.87, and 0.18 kg CO2-equivalent kg−1 grain yr−1 for the CF, F-D-F, and F-RF, respectively. These results suggest that F-D-F could be used to maintain the grain yields and simultaneously mitigate the climatic impact of double rice-cropping systems.