The impact of cell voltage on the capacitance of practical electrochemical supercapacitors is a phenomenon observed experimentally, which lacks a solid theoretical explanation. Herein, we provide combined experimental and molecular dynamics investigation of the relation between voltage and capacitance. We have studied this relation in supercapacitor cells comprising of activated carbon material as the active electrode material, and neat ionic liquids (ILs), and a mixture of ILs as the electrolyte. It has been observed that the increase of accumulative charge impacts the conformation and packing of the cations in the anode, which determines its nonlinear behavior with increasing voltage. It has also been shown that for the mixture IL with two types of cations, the contribution of each type of cation to the overall capacitance is highly dependent on the different pore sizes in the system. The smaller tetramethylammonium (TMA + ) shows tendency for more efficient adsorption in the mesopores, while 1-Ethyl-3-methylimidazolium (EMIM + ) is found to be present almost exclusively in the micropores where TMA + is present in small quantities. Such microscopic insights from computer simulations of the molecular phenomena affecting the overall performance in supercapacitors can help to design more efficient electrolytes and devices.