Magnesium ion battery (MIB) marks a notable progression in postlithium ion technology, leveraging the multivalent redox properties and abundance of magnesium. However, the challenges arising from polarizing effects of bivalent Mg 2+ ions on the anode restrict low-voltage Mg storage and insertion/ extraction kinetics. This computational investigation proposes a design strategy centered on intercalation chemistry, aiming to balance localized bonding and noncovalent interactions within the polarizable electronic cloud of a three-dimensional black phosphorus (BP) composite anode. Our findings reveal the critical role of spacer groups in reducing through-space interlayer interactions mediated by the polarizable π electron cloud in van der Waals layered materials utilized as intercalation anodes. Through this structural engineering approach, a substantial specific capacity is achieved, ranging from 1620 to 1644 mAhg −1 at low voltage (0.10−0.45 V), while also promoting rapid electron/ion transfer kinetics across high states-of-charges. Subsequently, we illustrate the underlying quantum mechanism by which the spacer group enhances the energy and rate performance of the Mg ion anode. The knowledge acquired from this study reaches far beyond MIBs, providing valuable implications for multivalent chemistry research affected by electronic polarization effects.