Soil organic carbon (SOC) is the most often reported attribute and is chosen as the most important indicator of soil quality and agricultural sustainability. In this review, we summarized how cultivation, crop rotation, residue and tillage management, fertilization and monoculture affect soil quality, soil organic matter (SOM) and carbon transformation. The results confirm that SOM is not only a source of carbon but also a sink for carbon sequestration. Cultivation and tillage can reduce soil SOC content and lead to soil deterioration. Tillage practices have a major effect on distribution of C and N, and the rates of organic matter decomposition and N mineralization. Proper adoption of crop rotation can increase or maintain the quantity and quality of soil organic matter, and improve soil chemical and physical properties. Adequate application of fertilizers combined with farmyard manure could increase soil nutrients, and SOC content. Manure or crop residue alone may not be adequate to maintain SOC levels. Crop types influence SOC and soil function in continuous monoculture systems. SOC can be best preserved by rotation with reduced tillage frequency and with additions of chemical fertilizers and manure. Knowledge and assessment of changes (positive or negative) in SOC status with time is still needed to evaluate the impact of different management practices.