Silicon dioxide (SiO₂) crystal serve as a relevant reference material in sputtering processes due to their well-defined properties and wide range of applications in material science. These crystals provide a stable and reproduceable target for sputtering, enabling the accurate calibration of sputtering equipment and the standardization of experimental conditions. The system stability in this process is particularly crucial in the development of thin films, coatings, and semiconductor devices, where precise control over material properties is essential [1]. The objective of this study is to explore the atomic layer structure and the composition of SiO₂ surfaces at different thicknesses from both experimental and numerical point of views. We first measure depth profiles of different thicknesses of SiO2 using Low Energy Ion Spectroscopy (LEIS) at various energies. LEIS is a highly surface sensitive technique which probes only the top atomic layer of a material surface [2]. Our findings indicate that combining sputtering with LEIS is an effective technique for probing the in-depth structure of SiO2 crystals grown on Si substrates. Distinct profile variations were observed for different surface oxidation processes, including O2 plasma, thermal oxide, and native oxide, particularly for oxide thicknesses varying between 1.2 to 2 nm. In contrast, for thicker oxides up to 30 nm, the profiles converged, showing minimal dependence on the oxidation method employed. To provide additional physical insights into the obtained depth profiles by LEIS measurements, we subsequently perform sputtering simulations using SDTrimSP [3]. Sputtering simulations calculate the interaction between incident ions and surface atoms and describe sputtering, as well as surface degradation and ion implantation in the target material. For Ar+ simulations demonstrate preferential sputtering of oxygen compared to silicon and suggest a layer intermixing in SiO2 of 1.2 nm for 0.5 keV incident ion energy and 3.2 nm for 2 keV incident ion energy. Our simulations further show that simulated sputtering depth profiles correlate well with the depth profiles obtained by the LEIS measurements. Ultimately, the well-established stoichiometry of SiO₂ will be used as a reference for oxygen content by integrating experimental measurements with simulation results. This method will enable quantification with LEIS for any material surface that contains oxygen. [1] Kelly, J. J. (2003) "SiO2: A Versatile Reference Material for Sputtering and Thin Film Research." Journal of Vacuum Science & Technology A, vol. 21, no. 4. [2] Brongersma, H. H., Draxler, M. (2007). Surface composition analysis by low-energy ion scattering. Surface Science Reports, 62(3), 63-109. [3] Mutzke, A. et al. (2019) “SDTrimSP Version 6.00”