In this study, mercury intrusion porosimetry (MIP) and X-ray micro-computed tomography (XRμCT) were used to characterize the pore structures and investigate the permeability characteristics of clay after aging and contamination with diesel. The results of the MIP tests showed that aging leads to reductions in porosity and average diameter, as well as an increase in tortuosity. The XRμCT analysis yielded consistent results; it showed that aging renders pores more spherical and isotropic and pore surfaces smoother. This weakens the pore connectivity. Micromorphological analysis revealed that aging led to the rearrangement of soil particles, tighter interparticle overlapping, and a reduction in pore space. The combination of MIP and XRμCT provided a comprehensive and reliable characterization of the soil pore structure. An increased diesel content increased the porosity and average diameter and reduced the tortuosity of the pores. Mechanistic analysis showed that aging weakens interparticle cohesion; this causes large agglomerates to break down into smaller agglomerates, resulting in a tighter arrangement and a subsequent reduction in porosity. An increase in diesel content increases the number of large agglomerates and pore spaces between agglomerates, resulting in increased porosity. Both aging and diesel content can weaken the permeation characteristics of soil.