The formation process of microstructures in cement pastes was first simulated with a numerical model. The simulated masses of the Ca(OH)2 and C-S-H phases were verified by measuring values with thermogravimetry-differential scanning calorimetry (TG-DSC) and XRD-Rietveld analysis. Then, the main transport paths for corrosive media, including nano-scale C-S-H gel pores, micro-scale capillary pores and the interface transition zone, were extracted, and the corresponding effective transport coefficients were determined. Finally, a multi-scale transport model ranging from the nano-scale through the micro-scale and to the macro-scale of concrete was established based on the porous media mechanics and multi-scale method, combined with numerical calculation and 3D visualization. This model will help to design and predict the service life of concrete structures.