Soil is composed of particles that are condensed and bonded under an overburden pressure during burial. Obtaining the permeability coefficient of soil particles is an important issue in geological, geotechnical and hydraulic engineering. The permeability coefficient has been traditionally obtained by fitting data based on the particle size gradient and soil porosity. However, it is difficult to measure soil porosity, sample at certain depths and maintain the original pressure while sampling in the field and performing tests in the laboratory. The complicated nature of the experimental method results in considerable uncertainty regarding the accuracy of the permeability coefficient. In this paper, soil particles bonded by the force of gravity are modeled, with different pressures at different depths. Permeable soils form at certain depths, and the macroscopic permeability coefficient of the soil is obtained via seepage calculations. A relationship between the upper pressure and the permeability coefficient is established to remove the dependence on the porosity, which is an intermediate coupling parameter between soil particles and seepage. The results show that the modeled permeability coefficient is consistent with the results of previous models, and the permeability coefficient decreases with increasing depth. Thus, the proposed model of soil particle penetration can be directly used to calculate the permeability coefficient.