Spinel manganite is considered as the most promising pseudocapacitive material due to its typical battery-type electrochemical behavior and high theoretical capacitance; however, understanding its structure−property relationship at the atomic level is still vague. In this study, the substitutional cation-related and geometrical site-dependent charge storage properties in the alkaline electrolyte have been systematically investigated by replacing the Mn with Co and Zn. Structure characterizations and electrochemical analysis clearly revealed the critically important role of octahedrally coordinated Mn in improving the electrode's charge storage capability. The Zn substitution results in dominant occupation of Mn in octahedral interstices and 3.5× enhanced specific capacitance at a current density of 1 A/g, whereas the Co ions occupy both octahedral and tetrahedral interstices with slight increment (18%) of the specific capacitance. However, the bimetallic compositional feature of CoMn 2 O 4 enables better capacitance retention rate and excellent cycling performance; in contrast, the Zn incorporation may lead to a distorted local structure and affect ion diffusion. Therefore, choosing substitutional cations with appropriate size and strong affinity to tetrahedral sites would be beneficial to improve the electrode's electrochemical charge storage properties. In general, our work not only provides a fundamental understanding of the geometrical site-dependent activity in spinel manganites but also summarizes the general principle in optimizing the electrode's charge transfer and ion diffusion processes, which can guide the synthesis of more spinel oxides with improved charge storage capability.