Stubble return, drainage, and tillage are common practices in rice agriculture, but their integrated effects in the winter season on greenhouse gas (GHG) emissions and soil organic carbon (SOC) and total nitrogen (STN) sequestration remain poorly known. A six-year experiment was carried out in a double-rice field to measure CH₄ and N₂O fluxes and SOC and STN contents, and then the net global warming potential (GWP) and yield-scaled GWP were estimated. Shifting the fields from no management in tradition to tillage in the winter season tended to reduce total CH₄ emissions of double-rice seasons by 14.7%, and it significantly decreased the emissions by 28.3% under drainage conditions. An additional reduction of 27.3% was further found without returning stubble. Therefore, winter tillage and drainage substantially reduced total GWP by 28.0%, in particular, a larger decrease (47.2%) was observed by no stubble return though N₂O emissions were strongly stimulated by 82.1%. Moreover, winter tillage significantly reduced SOC sequestration rate while played little role in STN sequestration rate. However, winter tillage with stubble return (2.5–4.1 t ha⁻¹) under drainage conditions showed the largest SOC (1.58 t C ha⁻¹ yr⁻¹) and STN (0.15 t N ha⁻¹ yr⁻¹) sequestration rates. Therefore, the net GWP and yield-scaled GWP were significantly decreased by 227% and 30.5%, respectively. Overall, our results suggest that winter drainage and tillage with stubble incorporation would be an effective management strategy to promote soil C and N sequestration and mitigate GHG emissions from the double-rice fields.