Applying electric fields to promote water/oil recovery efficiency is gaining increasing attention in downstream of heavy oil development. In this work, molecular dynamics simulations were performed to study the motion of N-(1-Hexylheptyl)-N′-(5-carboxylicpentyl) perylene-3,4,9,10-tetracarboxylic bisimide (C5Pe) between kaolinite (Kaol) surfaces mediated by external electric field in water under different pH. Aggregation of C5Pe was mainly mediated by pH and not affected by the electric field, while adsorption responded to both pH and the electric field. In neutral and alkaline solutions, C5Pe was deprotonated, and its distribution between two Kaol surfaces was mainly mediated by the Coulombic force exerted by the electric field. In acidic solutions, C5Pe carried zero charge, and yet its distribution was still affected by the electric field. The external electric fields mediated the wettability of the two Kaol surfaces in different extents, and C5Pe preferred to adsorb on the more hydrated surface. The mediation of the electric fields on the wettability of surfaces was achieved in two stages. In the first stage, when the electric field of a low strength was applied, diffusion of water enhanced. The hydration of both Kaol surfaces became increased as water molecules formed more hydrogen bonds with the surfaces. As the electric field strength became sufficiently high, diffusion showed no further enhancement, and the re-orientation of water dipoles started dominating the hydrogen bonding with the surfaces. Carrying opposite charges, the hydrogen bond donors and acceptors of water were differently regulated by the electric field, and therefore water molecules conformed in a certain manner under the electric field of high strength. As a result, the hydrogen bonding between water and the two Kaol surfaces (placed on two sides of the simulated box under the electric field) varied with their positions. Due to the structural hindrance of the hydroxyl groups on the surface, the surface could provide more hydrogen bonding donors formed more hydrogen bonds with water, and thus became more hydrophilic and had stronger attraction to C5Pe.