The importance of soil organic carbon (SOC) sequestration in agricultural soils as climate-change-mitigating strategy has become an area of focus by the scientific community in relation to soil management. This study was conducted to determine the temporal effect of different tillage systems and residue management on distribution, storage and stratification of SOC, and the yield of rice under double rice (Oryza sativa L.) cropping system in the southern China. A tillage experiment was conducted in the southern China during 2005–2011, including plow tillage with residue removed (PT0), plow tillage with residue retention (PT), rotary tillage with residue retention (RT), and no-till with residue retention on the surface (NT). The soil samples were obtained at the harvesting of late rice in October of 2005, 2007 and 2011. Multiple-year residue return application significantly increased rice yields for the two rice-cropping systems; yields of early and late rice were higher under RT than those under other tillage systems in both years in 2011. Compared with PT0, SOC stocks were increased in soil under NT at 0–5, 5–10, 10–20, and 20–30 cm depths by 33.8, 4.1, 6.6, and 53.3%, respectively, in 2011. SOC stocks under RT were higher than these under other tillage treatments at 0–30 cm depth. SOC stocks in soil under PT were higher than those under PT0 in the 0–5 and 20–30 cm soil layers. Therefore, crop residues played an important role in SOC management, and improvement of soil quality. In the 0–20 cm layer, the stratification ratio (SR) of SOC followed the order NT>RT>PT>PT0; when the 0–30 cm layer was considered, NT also had the highest SR of SOC, but the SR of SOC under PT was higher than that under RT with a multiple-year tillage practice. Therefore, the notion that conservation tillage lead to higher SOC stocks and soil quality than plowed systems requires cautious scrutiny. Nevertheless, some benefits associated with RT system present a greater potential for its adoption in view of the multiple-year environmental sustainability under double rice cropping system in the southern China.