The electrowetting and permeation behaviors of ionic liquids, which enable the control of their transport at low flow rates without external mechanical forces, significantly promote the development of microfluidic technology. A micro-valve system developed with the combination of porous substrates and micro-channels allows the control of ionic liquid on–off states and the adjustment of its flow rates solely using electrical energy. However, the nanoscale mechanisms of electrowetting of ionic liquid clusters on the surface of porous materials have not been fully revealed. In this study, molecular dynamics simulations are employed to investigate the impact of substrate wettability, pore characteristics, electric field features, and ionic liquid types on electrowetting. The results indicate that the substrates should be maintained hydrophobic initially to decrease spontaneous permeation and avoid over-wetting. Increasing the electric field strength promotes permeation, but an excessively intense electric field intensifies the ion field evaporation. Furthermore, the electrowetting and permeation mechanisms of various substrate pore sizes and pore spacings can be explained by the motion characteristics of cations and anions. Kinematic analysis of the ionic liquids climbing the capillary sidewalls under an alternative electric field at a controllable velocity is provided. These conclusions can provide theoretical guidance and reference for the electrowetting and permeation of ionic liquids.