Surface chemistry plays a critical role in the ion structuring of ionic liquids (ILs) at the interfaces of electrodes and controls the overall energy storage performance of the system. Herein, we functionalized the gold (Au) colloid probe of an atomic force microscope with −COOH and −NH2 groups to explore the effect of different surface chemical properties on the ion structuring of an IL. Aided by colloid-probe atomic force microscopy (AFM), the ion structuring of an imidazolium IL, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6], abbreviated as BP hereafter), on the Au electrode surface and the ion response to the change in the surface chemistry are investigated. AFM morphologies, contact angles, and approaching force–distance curves of the BP IL on the functionalized Au surfaces exhibited that the IL forms a more obvious layering structure on the −COOH-terminated Au surface (Au–COOH), while it forms heterogeneous and aggregating droplets on the −NH2 surface (Au–NH2). The formed uniform and aggregation-free ion layers in the vicinity of the Au–COOH surface are due to the π–π+ stacking interaction between the delocalized π+ electrons from the imidazolium ring in the IL [BMIM]+ cation and the localized π electrons from the sp2 carbon on the −COOH group. The in situ observation of nano-friction and torsional resonance frequency at the IL–electrode interfaces further demonstrated the ion structuring of the IL at Au–COOH, which results in a more sensitive electrochemical response associated with a faster capacitive process.