Evolution of soil-water movement patterns following rare and extreme rainfall events in arid climates is not well understood, but it has significant effects on water availability for desert plants and on the hydrological cycle at small scale. Here, field data and the Hydrus-1D model were used to simulate the mechanisms of soil water and vapor transport, and the control factors associated with temporal variability in the soil water and temperature were analyzed. The results showed that thermal vapor transport with a no rainfall scenario determined daily variability in water content at the soil surface. During rainfall, isothermal liquid water fluctuated as a result of dry sandy soils and matric potential in the upper soil (0–25 cm), and thermally driven vapor played a key role in soil-water transport at 40–60 cm soil depth. After an extreme rainfall event, thermal vapor flux increased and accounted for 11.8% of total liquid and vapor fluxes in daytime with a steep temperature gradient; this was very effective in improving long-term soil-water content after the rain. The simulated results revealed that thermal water vapor greatly contributed to the soil-water balance in the vadose zone of desert soil. This study provided an alternative approach to describing soil-water movement processes in arid environments, and it increased understanding of the availability of water for a desert plant community.