Abstract: The compositions of soils are various. Particularly, the scale of the soil structure is large. Both multi-material and multi-scale have an effect on the structural characteristics of soils. Based on the indoor experiments (MIP, SEM and X-μCT) and numerical simulation tests (data constrained modeling, abbreviated as DCM), the multi-scale structure of multi-component in the consolidation process of saturated fine-grained soil is studied. In addition, 3D structure of saturated fine-grained soil is analyzed quantitatively. This study focuses on studying the changing mechanism of soil structure in the process of consolidation. The results show that the pressure reaches 400 kPa approximately when the saturated fine-grained soil begins to creep. The corresponding critical value of pore diameter is 0.4 μm (micrometer-pore). The pore and pore cluster quantities increase with the increasing pressure and then decrease. Beyond this value, there is no noticeable change. However, the change rules of pore and pore cluster are not entirely consistent. The quantities of pore and pore cluster reach the peak at pressure up to 200 kPa and 400 kPa, respectively. The methods in this study are not only applied in saturated fine-grained soil, but also contributes to further study on the micro-macroscopic mechanics of other materials. The DCM may become a breakthrough when analyzing the structure of other soil materials. Thus, the quantitative characterization of various soil structures may be achieved.