The effect of different tillage systems on the soil organic carbon (SOC), active organic carbon (AOC) and remaining organic carbon (ROC) were studied in a long-term experiment in Chongqing, China. The experiment included five tillage treatments, which are conventional tillage with rice only system (DP), conventional tillage with rotation of rice and rape system (SH), 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), respectively. The results showed that the content of SOC declined as the soil depth increased, and presented obvious surface enrichment phenomenon under the no-tillage systems. The order of SOC, AOC, ROC and ROC/SOC in the 0–60 cm soil layer under different tillage systems was LM (22.74 g kg-1) > DP (14.57 g kg-1) > XM (13.73 g kg-1) > LF (13.10 g kg-1) > SH (11.92 g kg-1), DP (3.67 g kg-1) > LF (3.49 g kg-1) > LM (3.28 g kg-1) > XM (3.17 g kg-1) > SH (2.69 g kg-1), LM (18.09 g kg-1) > DP (10.34 g kg-1) > XM (10.12 g kg-1) > LF (9.20 g kg-1) > SH (8.80 g kg-1) and LM (85%) > SH (78%) > XM 77%) > LF (75%) > DP (74%). Compared with other systems, LM significantly increased SOC, ROC and ROC/SOC, which indicated long-term LM system performed good effect for carbon sequestration.