Electroconductive metal-organic frameworks (MOFs) have emerged as high-performance electrode materials for supercapacitors, but the fundamental understanding of the underlying chemical processes is limited. Here, the electrochemical interface of Cu3(HHTP)2 (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene) with an organic electrolyte is investigated using a multiscale quantum-mechanics/molecular-mechanics (QM/MM) procedure and experimental electrochemical measurements. Our simulations reproduce the observed capacitance values and reveals the polarization phenomena of the nanoporous framework. We find that excess charges mainly form on the organic ligand, and cation-dominated charging mechanisms give rise to greater capacitance. The spatially confined electric double-layer structure is further manipulated by changing the ligand from HHTP to HITP (HITP = 2,3,6,7,10,11-hexaiminotriphenylene). This minimal change to the electrode framework not only increases the capacitance but also increases the self-diffusion coefficients of in-pore electrolytes. The performance of MOF-based supercapacitors can be systematically controlled by modifying the ligating group.