Surface sputtering and structural modifications induced in silicon dioxide thin films (SiO2/Si) deposited on silicon substrates and irradiated by swift (10–40 MeV) heavy Auq+ (q = +4, +6, +7, and +9) ions were investigated by grazing‐incidence X‐ray diffraction (GIXRD) spectroscopy, Rutherford backscattering (RBS) spectrometry and time‐of‐flight elastic recoil detection (ToF‐ERDA) technique. The GIXRD analysis of the as‐deposited and irradiated samples revealed increasing structural modifications of the SiO2 thin films under Auq+ ion impacts with increasing ion‐beam energy. The changes consisted of decreased grain sizes with increased strain accompanied by a phase transformation from crystalline to amorphous films. RBS analysis showed a decrease in the mean stoichiometric (O/Si) ratio from (2.2 ± 0.1) to (1.7 ± 0.1), due to preferential sputtering of oxygen, as the incident ion energy increased. The obtained RBS‐results were then completed by those of ToF‐ERDA analysis technique using a 40 MeV Au9+ heavy ion beam. The preferential sputtering yield ratios (YSi/YO) were determined experimentally both versus electronic stopping power and ion fluence. The obtained results were then compared to numerical values derived from the inelastic thermal spike (i‐TS) model, Sigmund's analytical formula and SRIM simulation code. A good agreement was observed between the measured preferential sputtering data and the i‐TS calculated values, when considering both nuclear elastic and electronic inelastic collision mechanisms. Besides, a close correlation is observed between the electronic stopping power dependent measured sputtering yields and the XRD peak intensity degradation per unit fluence. These observations suggest that the same mechanism of MeV heavy ion‐irradiation induced extended atomic disordering, occurs both in the case of structural modifications and surface sputtering. Finally, the obtained experimental results are discussed on the basis of the i‐TS model.