Damages caused by ion beam irradiation during S-SIMS measurements of polymer samples such as polytetrafiuoroethylene (TEFLON), polyethyleneterephthalate (PET) and polycaprolactam (NYLON6) were investigated by using TOF-SIMS, QSIMS and XPS. Intensity changes of each secondary ion species vs. ion dosage were analyzed from the view point of chemical structures of the samples. Changes of surface chemical structures due to ion bombardments were also investigated via curve fitting and quantification of the observed XPS spectra. The results were discussed with the aid of semiempirical MO calculations, which proved to be useful for the qualitative interpretation of the chemical state change analyzed by XPS and the origin of the major peaks in the S-SIMS spectra.