In this study, we have observed structural change of self-assembling nonionic pentaethylene glycol monododecyl ether (C12E5) surfactant formed on a potential-controlled highly oriented pyrolytic graphite (HOPG) surface by electrochemical frequency modulation atomic force microscopy (EC-FM-AFM). At a negative and a positive potential side with respect to the point of zero charge (pzc), a periodic hemicylindrical structure is formed on the whole surface, while a disordered single-layered thin film is formed at a potential around the pzc. This demonstrates that the electrochemical tuning of the electrode potential enables precise control of the nonionic self assembly structure. We also found that the self-assembly structure is expanded by Na+ ion contained in C12E5 solution. This can be reasonably explained by selective cation binding of a C12E5 molecule like a crown ether. In addition, we estimated a response time of phase transition between the two phases by electrochemical impedance measurement.