MXene nanomaterials have attracted great interest as the electrode of supercapacitors. However, its energy storage mechanisms in organic electrolytes are still unclear. This work investigated the size effect of cations (i.e., Li+, Na+, K+, and EMIM+) on the capacitive behaviors of MXene-based supercapacitors. The experimental results demonstrate that the specific capacitance increases obviously with decreasing cation size (i.e., from 43 F g−1 (EMIM+) to 129 F g−1 (Li+) at 2 mV s−1). Density-functional theory calculation reveals a correlation between cation size and ion–electrode surface interaction, supporting experimental observations of the capacitive-dominant behavior. Molecular dynamics simulations reveal that the ionic solvation structure and desolvation degree of intercalated cations as a function of solvation size, providing dynamic insights into the experimentally observed specific capacitance trends. Our comprehensive experimental and computational study provides valuable insights into the intricate solvation effects governing the charge storage mechanisms. This finding of ion dynamics, solvation structure, and desolvation may contribute to guide the design and optimization of appropriate ions/electrolytes combinations for MXene-based supercapacitors.