Germanium suboxide films and GeO/SiO2 multilayer heterostructures deposited onto Si(001) substrates using evaporation in high vacuum were modified using irradiation of 167 MeV Xe+26 ions with fluences varying from 1011 to 1013 cm−2. According to Raman spectroscopy data, the swift heavy ion irradiation does not lead to the expected decomposition of germanium suboxide in germanium nanoclusters and GeO2. Infrared absorption spectroscopy measurements show that under irradiation the GeO/SiO2 layers were intermixed with formation of Ge-O-Si bonds. We report strong photoluminescence in the visible range at room temperature, which is most probably due to Ge-related defect-induced radiative transitions. Moreover, a new infrared luminescence band (~0.8 eV) was observed in irradiated structures, which can be related to defects or defects complexes in GexSiyO2 glass.