Atomic force microscopy (AFM) with a gold colloid probe modeled as the electrode surface is employed to directly capture the contact resonance frequency of two phosphonium-based ionic liquids (ILs) containing a common anion [BScB]− and differently lengthened cations ([P6,6,6,14]+ and [P4,4,4,8]+). The comparative interfacial studies are performed by creating IL films on the surface of gold, followed by measuring the wettability, thickness of the films, adhesion forces, surface morphology and AFM-probed contact resonance frequency. In addition, the cyclic voltammetry and impedance spectroscopy measurements of the neat ILs are measured on the surface of the gold electrode. The IL with longer cation alkyl chains exhibits a well-defined thin film on the electrode surface and enhanced the capacitance than the shorter chain IL. The AFM contact resonance frequency and force curves reveal that the longer IL prefers to form stiffer ion layers at the gold electrode surface, suggesting the “…anion–anion–cation–cation…” bilayer structure, in contrast, the shorter-chain IL forms the softer cation–anion alternating structure, i.e., “…anion–cation–anion–cation…”.