In the existing research studies of hydraulic conductivity, most of them assume that soil consists of spheroidal particles and the value of hydraulic conductivity can be designated by the particle size. In the actual soil layers, the shape of soil particles is mostly ellipsoid or rod-like rather than ideal sphere. Therefore, the prediction of soil permeability using current method often deviates from the actual situation and cannot capture the anisotropy nature of soil without consideration of the effect of the axis size of soil particles in two different directions. To solve this problem, a new theoretical model with three different soil particle arrangements is introduced to derive a new hydraulic conductivity-particle size relationship considering the size difference in two directions. This model, from a microscopic perspective, divides pores into numerous pore units and obtains hydraulic conductivity of each tube unit, eventually predicting the permeability of soil layer based on an equivalence principle. The proposed equation is validated in comparison with experimental data from the existing literature and is proved to have a satisfied accuracy to predict hydraulic conductivity for a wide range of soils, from bentonite-silt mixed soils to sandy soils. The proposed model provides a new perspective for accurately predicting the hydraulic conductivity.