The present work proposes the use of two‐dimensional correlation mapping (2D‐CM) methods to analyze both particle induced X‐ray emission (PIXE) and Rutherford back scattering (RBS) spectra. RBS spectra of ion irradiated (H+ and He2+) poly(ether ether ketone) (PEEK) films were analyzed by both generalized and hybrid 2D‐CM techniques to reveal the chemistry involved in different ion irradiation types. The analysis indicated different irradiation mechanisms using He2+ and H+ high energy ion beams and was assigned to X‐linking and Y‐linking, respectively. The effects of sulfonation on the structure of PEEK membranes were also analyzed from their RBS and PIXE spectra. The sequential order of elemental concentration change with increasing the degree of sulfonation (DS) was determined as: N→S→O→C, and the origin of Nitrogen was assigned to the casting solvent as revealed from nuclear magnetic resonance (NMR) spectra. In addition, Hetro‐2D‐CM‐PIXE‐RBS analysis indicated the presence of three RBS Sulfur signals, and were assigned to Sulfur at surface, in the middle and in depth. 2D‐CM techniques could be considered as a promising approach to enrich information obtained by ion beam analysis.