Understanding the ionic liquid (IL)-electrode interface is imperative for the applications of supercapacitors or other electrochemical systems. Here, the electrical double layer transition and charging process of the ILs-based supercapacitor were explored by performing molecular dynamics simulations with the constant electrical potential method. The structure transition is first illuminated by the analysis of number density, ionic orientation, electrode charge distribution and ion displacement, showing the formation process of the electrical double layer. Meanwhile, the co-existing cation and anion in the interfacial region cause the electrode to possess a non-Gaussian charge distribution and the ionic displacement demonstrates that both the interfacial layer and the bulk liquid contribute to the total energy storage, which is a common feature of the ILs system, contrary to the conventional viewpoint. Furthermore, the interfacial layer thickness, charging time and average differential capacitance (at high voltage) all increase with the anion size (in the order of BF4--> PF6--> OTf--> TFSI(-)with the same cation of Bmim(+)), indicating that the larger anion can restrain the ionic movements and enhance the capacitance. The identified correlation between the charging mechanism and anion characteristic would be helpful for the molecular design of the ILs-electrode interface in the supercapacitors or other key chemical engineering applications.