The impact of conservation tillage practices on carbon sequestration has been of great interest in recent years. This experiment analyzed the organic carbon status of soils sampled at depth increments from 0 to 60 cm after 20 years in a purple paddy soil. The tillage experiment was established in the Key Field Station for Monitoring of Eco-Environment of Purple Soil of the Ministry of Agriculture of China, located in the farm of Southwest University (30°26′N, 106°26′E), Chongqing. In this paper, five tillage treatments including conventional tillage with rice only system (DP), conventional tillage with rotation of rice and rape system (SL), no-till and ridge culture with rotation of rice and rape system (LM), no-till and plain culture with rotation of rice and rape system (XM) and tillage and ridge culture with rotation of rice and rape system (LF) were selected as research objectives to measure SOC storage and stratification ratio of SOC (CSR). The SOC storage under different tillage systems was calculated based on an equivalent soil mass. The CSR can be used as an indicator of soil quality because surface organic matter is essential to erosion control, water infiltration, and the conservation of nutrients. Results showed that in soil under no-till SOC was concentrated near the surface, while in tilled soil SOC decreased equably with the increase of soil depth. The difference of SOC contents between the five tillage systems was the largest in the top soil and the lowest in the bottom soil. The order of SOC storage was LM (158.52 Mg C•ha-1) >DP (106.74 Mg C•ha-1) >XM (100.11 Mg C•ha-1) >LF (93.11 Mg C•ha-1) >SL (88.59 Mg C•ha-1), LM treatment was significantly higher than the other treatments. The CSR of 0-10/50-60 cm was 2.65, 2.70 and 2.14 under LM, XM and LF treatments, while 1.54 and 1.92 under DP and SL treatments. We considered CSR>2 indicate an improvement in soil quality produced by changing from tillage to no-tillage, as well as changing from plane to ridge. Overall, long-term LM treatment is a valid strategy for increasing SOC storage and improving soil quality in a purple paddy soil in Southwest China.