Abstract: Reinforced concrete structures are widely used in civil engineering, but chloride-induced corrosion is one of the major factors that seriously deteriorate the durability of reinforced concrete structures. Thus, many numerical models have been developed to study the ion transport of cement-based material in the previous papers. However, most of these models could not consider the interactions between ions in the pore solution and cement hydrate. Based on the transport essential process of chloride in cement-based materials, this research presents a multi-species ionic transport model for cement-based materials coupling ion-cement hydrate interactions. Firstly, both the surface complexation model and the phase-equilibrium model were used to simulate the ion-cement hydrate thermodynamic interactions. Moreover, operator splitting algorithm was employed to solve the finite element numerical model of Nernst-Planck equation that coupling the ion-cement hydrate interactions, and then the variations of the content of each phase in cement hydrate, the porosity and the concentration of free ion in pore solution were discussed. Finally, the multi-species ionic transport numerical model was preliminarily verified by the experimental data published in the previous paper.