<p>The wide distribution range and the high sensitivity to seasonal changes highlight the importance of hydro-mechanics of partially saturated soils. The key to correctly understanding lies in recognizing the correlation between soil microstructure and the macroscopic water retention characteristics. In this study, spherical glass beads were selected as a well-controlled model material to replace natural granular soils (such as sands), to obtain clearer statistics of the contact coordination between particles and water. The spatial distribution and morphology of the three phases (solid, water, and air) in a partially saturated granular material at five key suction states were obtained through X-ray tomography performed during drying, providing insights into the dynamic evolution of wetting connectivity and local particle environment. A three-dimensional simulation domain was then constructed from a cubic subvolume in the reconstructed tomographic image corresponding to the third suction level. The topological interfacial distribution during the drying process was reproduced through single-component multiphase Shan–Chen lattice Boltzmann modeling (SC-LBM). Compared to the experiments, LBM enables the monitoring of liquid migration of partially saturated materials during the drying process (from full saturation to complete dryness) at a lower cost. Based on the representative elementary volumes, a wide distribution of the micro-interfacial area was obtained, and the Bishop effective stress parameter was further calculated. These findings offer valuable insights for future investigations of partially saturated materials, particularly in capturing microscopic characteristics (such as fluid distribution, cluster coordination number, and interfacial area) and deriving macroscopic strength indicators (such as cohesive strength and the Bishop effective stress parameter).</p>