Solute diffusion in partially saturated porous media is an important fundamental process in many natural and environmental systems. At low water saturation, the solute transport is governed by the diffusion in thin water films on the surfaces of solids. In this study, we established an improved pore-scale simulation framework successfully describing the solute diffusion in variably saturated porous media (e.g., soils), which considers the contribution of the diffusion within the thin water film on the surface of the solid matrix. The model takes into account the liquid–gas distribution in the underlying porous media by the Shan-Chen lattice Boltzmann Method (LBM) and simulates the solute diffusion in the bulk liquid phase and the water film. Based on the numerical results, an easy-to-use theoretical formula was also developed to predict the effective diffusivity in microporous materials at low saturation levels. The average relative error of its prediction with respect to the experimental data from the literature is about 30%, while that of the classical power law exceeds 70%. A simple phase diagram was defined, which allows us to identify the situations under which it is necessary to take the influence of surface water films on the effective diffusivity in unsaturated microporous media into account. The present study improves the pore-scale model to address solute diffusion in the water films at low water saturation and elucidates the contribution of thin water films on solute transport.