Understanding the transport mechanisms within unsaturated porous media is essential to the durability problems associated with cement-based materials. However, the involvement of multi-ions electrochemical coupling effect, especially under unsaturated condition makes the transport mechanisms even more complex. In this study, the moisture and multi-ionic transport in unsaturated concrete have been modeled in three-dimensional cases. The contribution from both water vapor and liquid has been considered in moisture transport. By adopting the constitutive electrochemical law, the electrostatic potential induced by inherent charge imbalance was calculated. With parameter calibration, the numerical results agreed well with the experimental data, proving the validity of the presented model. Results from a parametric analysis showed that neglecting multi-ions coupling effect will lead to an underestimated chloride concentration, and saturated degree has an obvious impact on the coupling strength among different ions. In addition, the existence of coarse aggregates will not only block mass transport but also make the discrepancies between two-dimensional model and three-dimensional model results more obvious. Other findings which have not been reported in existing studies are also highlighted.