It is important to examine the roles of crop rotation systems and soil characteristic types (i.e., soil texture, soil type, soil parent materials) in influencing the soil organic carbon density (SOCD) variability in order to improve the carbon sequestration amount in agricultural soils. Based on the soil samples collected from farmlands of Xindu and Pixian in 2010, the effects of soil characteristics types and crop rotation systems on SOCD variability were compared quantitatively through variance analysis and stepwise regression analysis. Results showed that the soil characteristics types and crop rotation systems both had significant effects on SOCD variability. Soil texture played a dominant role and clay content had a significant positive correlation with SOCD at all soil layers (P<0.01). Compared to crop rotation systems, soil characteristics types played more important roles in influencing the SOCD variability, explaining 35.9%, 43.0% and 16.8% the SOCD variability in the soil layers 0–40cm, 0–20 cm (topsoil) and 20–40cm (subsoil), respectively. While the crop rotation systems were taken into consideration together with soil characteristic types, the SOCD varibility accounted for in the soil layers 0–40cm and 0–20cm only increased 2.2% and 4.5%. Thus, crop rotation systems played minor roles than soil characteristic types in regulating SOCD variability. To reveal the driving force of the farmland SOCD variability, the focus should be on the soil characteristic rather than on crop rotation systems.