Adsorption process and structure of perfluorosulfonated acid (PFSA) polymer on a highly oriented pyrolytic graphite (HOPG) surface were elucidated by an in situ tapping mode atomic force microscope (AFM). Micellar aggregates of PFSA polymers first randomly adsorbed on a bare HOPG surface, and then the adsorbed aggregates extended under the influence of atomic arrangement of HOPG Surface, to form two-dimensionally ordered domains.