Irradiation of argon, oxygen and nitrogen ion beams onto polyimide films was performed and the surface chemical structure was analyzed in detail by X-ray photoelectron spectroscopy (XPS). The acceleration voltages were 0.5, 1.5 and 3.0 kV for argon and nitrogen beams, and 0.1, 0.5, 1.5 and 3.0 kV for oxygen beam. The elemental ratios of oxygen, nitrogen and carbon were calculated from Is peaks of the corresponding elements. The results show that the content of oxygen and nitrogen in near-surface layer decreased after argon beam irradiation, while the ratios of oxygen and nitrogen increased after irradiation of oxygen and nitrogen ion beams, respectively, especially in the case of samples treated at low acceleration energies. These findings indicate that the oxygen and nitrogen atoms contained in polyimide films were selectively sputtered by the incident particles, and oxygen and nitrogen ions from the beams were incorporated into the film. The spectra were deconvoluted into the component peaks and the ratios of these peaks were calculated. The XPS results show that the bonds originally contained in the polyimide structure were destroyed as a result of random collisions of the incident ions and the energy transfer to the atoms of polyimide. The XPS spectra after ion beam irradiation are related to the rearrangement of those recoil atoms and the ions incorporated into the film, and formation of new types of bond such as C-C-C, C-O-C and C-N-C.