To fully understand the solidification effect of metakaolin (MK) on Pisha-sandstone cement soil, unconfined compressive strength (UCS), ultradepth three-dimensional microscopy (U3DM), nuclear magnetic resonance (NMR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) tests were carried out on the solidified soil. The solidification mechanism of MK was comprehensively analyzed from the perspectives of macromechanics, mesostructure, and micromechanisms. From the perspective of macromechanics, the damage variable V tended to decrease with the increase in MK content, which indicates that the addition of MK helps improve the ability of the solidified soil to resist damage. From a mesoscopic perspective, the addition of MK reduced the average height difference of the surface of the solidified soil. The complexity of the size, number, distribution, and shape of pores in the solidified soil was comprehensively analyzed based on NMR experiments. With the increase in MK content, the proportion of pores with a pore radius > 1 µm decreased, while the fractal dimensions DT and D2 increased. XRD and SEM experiments show that the hydration products (calcium aluminate hydrate and calcium silicate hydrate) formed after the incorporation of MK were tightly combined with the soil particles and filled the pores. A gray entropy correlation analysis carried out to analyze the correlation effect of different pore structures on the strength of the solidified soil showed that the pore sizes of 0–0.1 µm had a large influence on the UCS. This is a valuable finding on the link between the microstructure and macromechanics of solidified soils.