Pore structure is closely related with strength, constitutive relation, consolidation characteristics, and permeability properties of soil. Consequently, improving the understanding of the relationship between microscopic structure and macroscopic physical and mechanical properties has extremely important scientific significance. A large number of studies have shown that pores of soil have fractal features, and hence, the carpet model can be used to approximately simulate the fractal structure of clay. In the present study, ANSYS software was selected to establish a microscopic model of clay to study the distribution of microscopic stress and microscopic deformation characteristics of pores under different consolidation pressures. Besides, the variation law of microscopic pore size was quantitatively determined by using IPP (Image-Pro Plus) software. Combined with the fractal theory, the changes of microscopic pore of numerical simulation and that of physical experiment during compression of clay are studied. All the results indicated that the microscopic stress distribution of clay is not uniform on the compaction process. The larger the pore size is, the bigger the compression stress on both sides and the greater the bending deformation of upper part of the pore is, which leads to the deformation of larger pores which is bigger than that of smaller pores. Based on the results, issues about the microscopic mechanism of the difference in vertical and horizontal permeability under compression of clay, the relationship between the changes of pore shape and microscopic stress, the preliminary principle of “preferential crush of larger particles” for granular soil, skeleton stress across the region where stiffness is relative larger, and the self-protection of particles and pores are also discussed. The results of this study are of great importance in understanding of soil compression and related physical and mechanical properties from the microscopic view.