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This paper looked at tillage impacts on net global warming potential (NGWP) soil organic carbon (SOC) change and indirect emissions (IE) on a double rice system in Southern China. Three treatments used in this study were no tillage with residue retention (NT), rotary tillage with residue retention (RT), and plow tillage with residue incorporation (PT). In respect of SOC sequestration, annual mean rates (0–20 cm) were not significantly different between tillage treatments averaging 2.89 MgC ha−1 yr−1 during 2005−2014.Two-year (2013–2014) measurement of GHGs showed NT tended to significantly decrease annual CH4, but increase N2O emissions in the paddy soil. The results suggested GHG mitigation and agricultural economic viability can be achieved by NT practice in double rice cropping systems.