An electrochemical cell combining the energy storage characteristics of the chemical redox reaction and a physical capacitor effect presents advantages including high energy and power densities, and long durability. In this study, we prepared nanohybrid materials between polyoxometalate (POM) and porous carbon, which have different porous structures and pore sizes, using different zeolitic templates. The POM molecules were loaded inside the porous carbon, and these POM/carbon nanohybrid materials were used as cathode active materials for lithium-ion batteries (LIBs). The performance of these molecular cluster batteries (MCBs) was significantly dependent on the porous carbon. Operando X-ray absorption fine structure (XAFS) and Li solid-state nuclear magnetic resonance (NMR) measurements of the POM/carbon-MCBs revealed that three-dimensional porous carbon with high surface areas can improve the performance. The results highlight the remarkable performance of porous carbon with a three-dimensionally-linked pore network structure as an additive for supercapacitors to realise high-performance energy storage devices.