In aluminum electrolysis, sodium penetration into carbon cathodes is considered as the main cause of cell failure and efficiency loss, but the detailed mechanism is still not definitely clear. Since the macroscopic properties of material depend on the microscopic structures, a large-scale atomistic model of anthracite cathodes was constructed to represent several important structural characteristics. Combined with Monte Carlo and molecular dynamics simulations, the adsorption and diffusion behaviors of sodium were investigated, respectively. The results suggest that sodium adsorption mainly occurs in the larger micro-pores with the range of 10–19 Å, while it accords well with to type-I Langmuir adsorption model. The sodium is found to be preferentially adsorbed in arch-like structures with 5- or 7-membered rings or around heteroatom, especially oxygen. Moreover, the movements of sodium through carbon matrix mainly depend on the continuous diffusive motion while most sodium particles tend to be trapped in voids with small mobility. The calculated transport diffusion coefficient is equal to 6.132 × 10− 10 m2/ s, which is in outstanding agreement with experimental results. This fundamental research would contribute to the understanding of sodium penetration mechanism and the optimization of cathode industry in the future.