Soil organic carbon (SOC) sequestration was evaluated for several long-term rain-fed cropping systems for conservation agriculture (CA) and conservation tillage (CT) in Cambodia using the Environmental Policy Integrated Climate (EPIC) model. The mean crop yield, biomass and SOC stocks of four treatments and three replication in each primary cropping system (rice, soybean and cassava) were used for calibration and validation during the period 2009–2013. The CT and CA1 treatments were assigned to continuous cropping of primary crops. CA2 and CA3 treatments were assigned to rotated primary crops with maize. In all CA treatments, forage or legume cover crops were prior planted and intercropped with the primary crops to maintain full soil cover. The results show that EPIC successfully simulated crop yields, biomass, and SOC. However, the model tended to underestimate SOC in the CT treatments and overestimate SOC in the CA2 and CA3 treatments. Crop residue was found to highly influence SOC sequestration. Sediment loss in the CT treatments was found to be four times greater than CA treatments due to the CT tillage effects. The 20-year future simulations, using historical weather and automatically generated by EPIC, showed a decrease trend in SOC stocks in all CT treatments and an increase trend in most CA treatments, with the greatest increase for CA2 and CA3 treatments. Thus, the CA treatments in combination with the maize rotation were demonstrated to be more efficient to manage SOC sequestration over CA with one continuous primary crop.