Self-assembly of ionic liquids (ILs) in solution has attracted wide attention due to their potential applications in various fields. The nature of counterions, especially aromatic counterions, will significantly affect the aggregation and morphological properties of ILs surfactants. In this paper, molecular dynamics (MD) simulations are applied to study the influence of three organic and inorganic counterions (phenolate (PO−), benzoate (BZ−), and Cl−) on the micellar structure of imidazolium (C14mim+) based ILs surfactant in aqueous solutions. Three micelles all possess prolate shape. The PO−, BZ−, and Cl− ions hardly affect the orientation and length of hydrophobic chains in micellar interior. Hydration numbers and average radial density distributions analyses show that interactions between micelles and water molecules are different in studied micelles. Surrounding water molecules penetrate into the deepest region in [C14mim][Cl] micelle. However, adsorbed Cl− ions are mainly located on micellar surface, not penetrating into micellar interior. Due to the intrinsic hydrophobicity of organic ions, both PO− and BZ− ions enter into deeper positions in micelles. Unlike Cl− ions, there exist π-interactions between adsorbed PO− and BZ− ions themselves. One interesting finding is that adsorbed PO− and BZ− ions can make micelle radius (Rg) increase but make solvent accessible surface area (SASA) decrease. Conversely, adsorbed Cl− ions make both Rg and SASA increase. Three MD models for different C14mim+ based micelles are proposed.