Vanadium diselenide (VSe₂) is a promising cathode material for magnesium–lithium hybrid batteries (MLHB), owing to its favorable electronic structure and layered framework. However, practical Mg²⁺ storage is hindered by narrow interlayer spacing, strong Mg²⁺ host Coulombic interactions, and structural degradation during repeated ion insertion. Here, we introduce a molecular interlayer engineering strategy based on ethylenediamine (EDA) intercalation to address these challenges. A combination of theoretical calculations and experimental investigations reveals that EDA modification simultaneously expands the interlayer spacing, modulates the electronic structure, and weakens the Coulombic interactions between the lattice and the guest ions, thereby facilitating Mg²⁺/Li⁺ diffusion and enhancing reaction kinetics. Moreover, the electron-rich –NH₂ groups of EDA engage in reversible chelation with the guest ions, providing additional storage sites and enabling an inorganic–organic synergistic storage mechanism based on topological intercalation reactions. As a result, the optimized EDA-intercalated VSe₂ (E(0.2)-VSe₂) cathode exhibits a stable capacity of 82.5 mAh·g⁻¹ over 4500 cycles at 1000 mA·g⁻¹, with a remarkable capacity retention of 72.7%. This work underscores molecular interlayer engineering as an effective strategy for enhancing the performance of layered cathodes in multivalent rechargeable batteries.