Abstract: The saturated fine-grained soil has a typical multi-scale three-dimensional overhead structure and its complex micro-morphology significantly affects the consolidation settlement and other macro-mechanical characteristics. Based on the scanning electron microscopy (SEM), a three-dimensional micro-model for saturated fine-grained soil with multi-scale structure is established by using the multi-energy synchrotron radiation X-ray micro-CT technology combined with the data constrained algorithm (DCM). The results show that the change trend of apparent porosity of soil surface is basically the same as that of volumetric porosity, while the apparent porosity is slightly smaller than the volumetric one. The pressure of 800 kPa is the turning point of apparent porosity of soil samples with pressure. It is presumed that the microstructure of soil changes remarkably at the pressure of 800 kPa, which may correspond to creep deformation of soil skeleton. The average pore shape coefficients of 100 kPa and 800 kPa are abnormal, lower than 0.32 at 100 kPa and significantly higher than 0.32 at 800 kPa, which indicates that the pore in soil is sensitive to pressure change at the initial stage of compression, while the soil structure changes at the later stage of consolidation. Both the volumetric porosity calculated by DCM and the apparent porosity of DCM two-dimensional slices are slightly lower than the experimental porosity of soil samples. The average apparent porosity of soil samples obtained by DCM two-dimensional slices fluctuates in the range of 0.35 to 0.45.The DCM may break through the resolution limitation and realize the characterization of micro-nanoparticles. Meanwhile, the DCM tested by the PCAS can provide a new way to calculate soil porosity.