The effect of carbonation on the concentration of free chloride ions in cement paste and the microstructure characteristics of the ions were studied using microscopic images of X-ray diffraction (XRD) and scanning electron microscope (SEM). The results showed that the influence of water-cement ratio on the concentration of free chloride ions before carbonation was affected by the concentration of total chloride ions. The higher the total chloride ion concentration was, the greater the effect of water-cement ratio on free chlorine concentration was. Carbonation had an adverse effect on the binding of chloride ions based on two reasons. First, carbonation promoted the decomposition of Friendel salt and reduced the amount of ion chemical curing. Second, due to the decrease of the amount of C-S-H in the hydration product, a large amount of Ca2+ was consumed, so the Ca/Si ratio reduced, which weakened the physical absorption ability, and reduced the adsorption amount of ions, therefore increased the concentration of free chloride ions in cement paste. The results suggest that carbonation can significantly refine pore structure and reduce porosity, which is conducive to weakening the diffusion and erosion of free chloride ions.