Abstract: The infiltration process in the vadose zone is affected by many factors. A quantitative study of the influence of the layered heterogeneous lithological structure and infiltration rate on the process of water infiltration in the vadose zone is helpful in selecting a single-phase flow model or water-gas two-phase flow model for simulating the infiltration process in the vadose zone under different conditions. In this study, combined with stratum conditions of landfills and other sites and the infiltration characteristics of polluted or waste water, water infiltration single-phase flow and water-gas two-phase flow models are established under the “upper fine and lower coarse” and “upper coarse and lower fine” layered heterogeneous lithological structures of the vadose zone, in order to discuss the applicability of the models under different layered heterogeneous lithological structures. Based on the “upper coarse and lower fine” lithological structural model, the influence of infiltration rate on the results of water-gas two-phase migration is further explored. The results based on paper models show that (1) under the “upper fine and lower coarse” lithological structure condition of the vadose zone, the influence of the gas phase can be ignored and the single-phase flow model can be used to simulate water migration in the vadose zone. Under the settings of the “upper coarseness and lower fineness” lithological structure, the fixed bottom pressure and no precipitation infiltration before the leakage of sewage and wastewater in this model, gas phase has a significant impact on the water migration when the permeability ratio of the upper and lower media in the vadose zone is greater than about 16 times, and the lower the permeability of the underlying medium and the greater the permeability ratio of the upper and lower media, the greater the difference between the results of the single-phase flow and water-gas two-phase flow. It is necessary to use the water-gas two-phase flow model to simulate the water migration in the vadose zone. (2) Under the “upper coarseness and lower fineness” lithological structure condition of the adose zone, the greater the infiltration rate, the stronger the blocking effect of air on the water infiltration, and the water-gas two-phase flow model should be used to simulate the process of water migration in the vadose zone.