The water table fluctuations can cause a reciprocating advection of soil gas in the vertical direction, known as vadose zone breathing. In this study, we developed a vadose zone breathing-facilitated vapor intrusion (VI) model and applied it to evaluate the influence of NAPL (non-aqueous phase liquid)-impacted soils. The developed model was first validated with data from previously conducted sand tank experiments and then used to simulate VI scenarios involving different fluctuation amplitudes and periods of the water table, soil types, building structures, and source depths. Our results suggest that within one month of vadose zone breathing (amplitude of 0.5 m and period of 4 d), the indoor pollutant concentration varies by approximately seven orders of magnitude, and the averaged concentration is nearly nine times larger than the steady-state concentration. The results also show that with the increase of mean soil particle size, the indoor pollutant concentration tends to increase and becomes more sensitive to vadose zone breathing; compared to the basement foundation, buildings with a slab-on-grade foundation are less susceptible; when the source depth exceeds 10 m, the source depth plays an insignificant influence. Our findings highlight that vadose zone breathing can promote the VI risks of buildings with a basement foundation at sites with shallow water tables, significant groundwater fluctuations, and coarse-textural soils.