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The two-phase seepage fluid (i.e., air and water) behaviors in undisturbed granite residual soil (U-GRS) have not been comprehensively studied due to a lack of accurate and representative models of its internal pore structure. By leveraging X-ray computed tomography (CT) along with the lattice Boltzmann method (LBM) enhanced by the Shan–Chen model, this study simulates the impact of internal pore characteristics of U-GRS on the water–gas two-phase seepage flow behaviors. Our findings reveal that the fluid demonstrates a preference for larger and straighter channels for seepage, and as seepage progresses, the volume fraction of the water/gas phases exhibits an initial increase/decrease trend, eventually stabilizing. The results show the dependence of two-phase seepage velocity on porosity, while the local seepage velocity is influenced by the distribution and complexity of the pore structure. This emphasizes the need to consider pore distribution and connectivity when studying two-phase flow in undisturbed soil. It is observed that the residual gas phase persists within the pore space, primarily localized at the pore margins and dead spaces. Furthermore, the study identifies that hydrophobic walls repel adjacent fluids, thereby accelerating fluid movement, whereas hydrophilic walls attract fluids, inducing a viscous effect that decelerates fluid flow. Consequently, the two-phase flow rate is found to increase with then-enhanced hydrophobicity. The apex of the water-phase volume fraction is observed under hydrophobic wall conditions, reaching up to 96.40%, with the residual gas-phase constituting 3.60%. The hydrophilic wall retains more residual gas-phase volume fraction than the neutral wall, followed by the hydrophobic wall. Conclusively, the investigations using X-ray CT and LBM demonstrate that the pore structure characteristics and the wettability of the pore walls significantly influence the two-phase seepage process.