Soil properties, such as wetting collapse behavior and permeability, are strongly correlated to the soil microstructure. To date, several techniques including mercury intrusion porosimetry (MIP), can be used to characterize the microstructure of soil, but all techniques have their own limitations. In this study, the features of mercury that penetrated and has been entrapped in the pore network of the specimens through MIP testing were investigated by X-Ray microtomography (X-μCT), in order to give an insight into the geometry of macropores and possible ink-bottle geometry. Two conditions of water content and density were selected for the compacted Maryland clay. The distribution and geometry features of mercury entrapped in the microstructure after MIP were characterized and pore size distributions were also reconstructed. The results suggest that, for the two conditions studied in this paper, macropores were evenly distributed within the specimens, and most of them with a non-spherical shape, and with aspect ratio (ratio between the maximum and minimum thickness along a given segment) smaller than three. Different dominant entrance pore size of macropore was obtained from MIP and X-μCT, due to the specific experimental protocol used in tests and the effect of ink-bottle geometry. Only the large pore bodies with high aspect ratio were imaged in X-μCT, due to the extrusion of mercury during the process of depressurization and subsequent sample preparation for X- μCT. But entire pore space was accessible in MIP. The difference in dominant entrance pore size was more significant for specimens with lower void ratio due to a more pronounced aspect ratio.