In this study we investigated the chemical and surface wettability changes of poly(dimethylsiloxane) (PDMS) induced by a 2.0 MeV He(+) beam irradiation. The chemical changes created in PDMS were characterized by universal attenuated total reflectance infrared (UATR-FTIR) spectroscopy, while the changes of the wettability were determined by contact angle measurements. In a separate analysis, hydrogen depletion was also investigated with a 1.6 MeV He(+) beam by applying the elastic recoil detection analysis (ERDA) and Rutherford backscattering spectrometry techniques simultaneously. The ERDA results showed that the hydrogen content of PDMS decreased irreversibly, which means that volatile products were formed under radiolysis, such as hydrogen or methane. The results were completed with UATR-FTIR measurements. We propose a complete reaction mechanism for the processes taking place in PDMS. These ion beam induced processes, such as chain scissions, cross-linking, and depletion of small molecular weight fragments, lead to the formation of a silica-like final product (SiO(x)). The significant chemical changes at the surface influence the wettability of PDMS, making it considerably more hydrophilic. The penetration depth of the 2.0 MeV He(+) ions is significantly higher compared to that of other surface modification techniques, which makes the modified layer thick and homogeneous; on the other hand, it is easily controllable by the energy of the incident ions.