Bimetallic spinel transition metal oxides play a major part in actualizing eco-friendly electrochemical energy storage systems (ESSs). However, structural precariousness and low electrochemical capacitance restrict their actual implementation in lithium-ion batteries (LIBs). To address these demerits, the sacrificial template approach has been considered as a prospective way to strengthen electrochemical stability and rate performance. Herein, metal-organic frameworks (MOFs) derived XMn2O4-BDC (H2BDC = 1,4-dicarboxybenzene, X = Zn, Co, Cu, Ni) are prepared by a hydrothermal approach in order to discover the effects of various metal cations on the electrochemical performance. Among them, ZnMn2O4-BDC displays best electrochemical properties (1321.5 mAh g−1 at the current density of 0.1 A g−1 after 300 cycles) and high efficiency with accelerated Li+ diffusivity. Density functional theory (DFT) calculations confirm the ZnMn2O4 possesses the weakest adsorption energy on Li+ with a minimized value of −0.92 eV. In comparison with other XMn2O4 through traditional fabrication method, MOF-derived XMn2O4-BDC possesses a higher number of Li+ transport channels and better electric conductivity. This tactic provides a feasible and effective method for preparing bimetallic transition metal oxides and enhances energy storage applications.