Abstract: The particles in the saturated fine-grained soils are small. Their specific surface areas are large. The pore water and organics in the soil tends to form aggregates. This combination has important influence on the physical and mechanical properties of the soil. In this paper, the effect of multi-material structure of saturated fine-grained soil on its consolidation and evolutionary properties is discussed from the perspective of three-dimensional microstructure. The components in the soil samples are classified into four groups:pores, organics, multi-minerals and illite-dominated minerals. The structures were analyzed by synchrotron radiation μCT combined with the data constrained modelling in the consolidation process. The results show that illite-dominated minerals are hydrophilic and displaya coexistence of multiple phases in a voxel with pore, so that the water is difficult to be discharged under high pressure(1600kPa).Organics combined with illite minerals form organoclay agglomerated particles. It is not only adsorbed on the illite-dominated mineral surface, but also embedded in the mineral structure. The organics migrated in consolidation progress, which is illustrated by gradually increased volume of organics(in 40~400μm diameter).The strength of the soil between the soil particles weakened. This research utilizes qualitative and quantitative analysis to obtain evolutionary characteristics of minerals and organics. The approach presented would be applicable in studying the relationship between microstructure and macro-properties for special engineering soils.