Calcium silicate hydrate (C-S-H) is the main hydration product of cement-based materials, which fundamentally affects the durability of concrete, such as chloride ion permeability. Since the structure and properties of C-S-H are closely related to the calcium to silicon ratio (Ca/Si), in this article, tobermorite and jennite models are combined to represent C-S-H with different Ca/Si ratios and their interface of the mixed phase. Atomic density distribution, ionic binding mode and Cl− ion dynamic states were employed. The results show that water molecules link the intralayer calcium ions to become the inner layer complex, and establish H-bond network together with the non-bridging oxygens and hydroxyl groups on the C-S-H surface to become the outer layer complex. Na+ ions replace free Ca2+ ions on the C-S-H surface to be adsorbed, and the latter can form Ca-Cl clusters by capturing Cl− ions after desorption. The diffusion coefficient of Cl− ions is larger in the low Ca/Si ratio C-S-H, and the adsorption amount of Cl− ions is larger in the high Ca/Si ratio C-S-H. In the interface of the mixed phases, Cl− ions tend to be adsorbed closely on the high Ca/Si ratio surface and away from the low Ca/Si ratio surface. Finally, a Ca/Si ratio gradient microstructure design for cement-based materials is proposed to prevent chloride ion penetration.