We report the ultrathin supercapacitor’s superior performance via the vertically aligned one-dimensional polyaniline structure (1D PANI) growth on the fluorine-doped tin oxide (FTO) substrate. FTO electrodes were treated by the molecular-self assembly, and the effects of different self assembled monolayers (SAMs) on both the evolution of PANI and electrochemical performance were examined. We obtained 809.09 F g−1 specific capacitance from ∼120 nm thick PANI (at 20 mV s−1 scan rate of cyclic voltammetry) via aniline blue water soluble SAMs modification. The supercapacitor’s internal dynamics were clarified by a new equivalent circuit model developed from the Graham model. Through the new model, accurate information about double-layer capacitance, percolation capacitance, and bulk capacitance, which composes the electrode’s capacitive performance, could be obtained. This work provided novel knowledge to develop PANI deposition and hence to achieve greater capacitances.