As the main product of hydration reaction of common Portland cement, calcium silicate hydrate (C-S-H) gel is a porous gel system containing capillary and gel pores. These channels act as transport channels for water molecules and ions in the cement system. The diffusion of water molecules and ions through C-S-H gel channels has significant effects on the strength, shrinkage, creep, chemical and physical reactions of the cement system. Polymer can modify cement-based materials and improve their ionic permeability resistance. In this study, emulsified asphalt powder (EAP) and vinyl acetate ethylene copolymer (VAE) redispersible polymer powder was added into the Portland cement mortar as admixtures, respectively. The influence of redispersible polymer powder on the transportation and erosion mechanism of ions in cement mortar was investigated by analyzing the pore structure, compressive strength ratio, chloride ion permeability depth and micromorphological of cement mortar. The adsorption and diffusion behaviors of ions with different concentrations and water molecules were explored by molecular dynamics simulation, and the physiochemical reactions between ions and hydration products during the transport process in cement-based materials were comprehended.