As a potential energy storage cell, the rechargeable magnesium (Mg) battery is limited by poor solid-state diffusion of Mg2+. Hence, the fundamental mechanisms between the electrolyte and the Mg electrode need to be deeply explored. In this work, a doped-Mg electrode/MgCl2 aqueous electrolyte system is constructed to explore the electrolyte structure and transport properties of ions through molecular dynamics simulations. Then, extensive simulations are conducted to study the effect of the doping levels on the electrode/electrolyte interface and ionic diffusivity. According to the number densities of different electrodes (i.e., Mg–Zn, Mg–Al, Mg–Si, and pure Mg), the Mg–Si electrode shows the strongest attraction to the ions in the electrolyte, indicating that the Mg–Si electrode can provide a higher ion storage performance. Moreover, the simulation results also show that the electrode capacitance presents a similar non-monotonic relationship with the increase of potential well depth under different doping ratios. At the doping ratio of 9%, the potential well depth has the strongest impact on the electric double layer (EDL) thickness compared with that of the other two doping ratios. The diffusion coefficient of water molecules weakly depends on the doping ratios and electrode materials. In contrast, the diffusion coefficient of ions varies strongly with the electrode materials, which could change up to 10–30% from its reference value (the diffusion coefficient of the Mg electrode system). This study will potentially provide an understanding of the influences of doped-Mg metal anodes on the structure and transport characteristics of Mg rechargeable batteries.