Soil structure is a fundamental property of soil fertility with its ability to transport water, nutrients and gas, and to provide habitat for microorganisms and fauna. Aggregated soil structure can improve agronomic productivity and increase the resistance to soil erosion. The formation of soil structure (or aggregates) is the result of biotic (i.e., microorganisms, fauna, roots) and abiotic (i.e., tillage, wetting and drying, freezing and thrawing, clay, ion) factors and their interaction. The relation between soil structure and biotic agents may be the key mechanism to sequester C in soil. Recently, to mitigate global change and to secure food safety, soil structure has received much attention. However, the manifold of interactions between soil structure and factors is still hardly quantified. On the other hand, soil structure and its stability are dynamics with these environmental factors. Although aggregate formation and stability have been investigated in numerous studies, aggregate is not a surrogate of soil structure. With new technology (i.e., micro CT, NEXAFS), the natural heterogeneity of the soil as a three-dimension porous system can be characterized possibly. It may provide us with a chance to fully understand soil structure formation, stability and its functions on C sequestration, water transport, and soil erosion.