To deeply understand the mechanical behaviors and evolution of nano-scale liquid bridge, the influence of variables such as initial particle spacing, the distance between solid-liquid surface and temperature on three-dimensional kaolinite-water system were analyzed by a combination of experiment, molecular simulation and theoretical equation. Studies have shown that initial distance between solid-liquid surface was the most sensitive to the breakage of liquid bridges, and the critical range was 15–20 Å. Due to the obvious stratification of water molecules, the calculated results were larger by Young-Laplace equation. By using surface energy to avoid contact angle and surface tension that are poorly defined on the microscopic level, the revised theoretical results were confirmed to be in good agreement with simulated data. The capillary force of kaolinite particles was mainly attributed to the contribution of negative pore water pressure, and nano-size liquid bridge can be considered to still obey the Young-Laplace equation. This work is crucial for the subsequent research on the water-holding properties of unsaturated soils.