To examine precise depth profiles at the interface of SiO2/SiC, a high resolution that can detect slight discrepancies in the distribution is needed. In this study, an experimental method to achieve a high resolution of less than 1 nm was developed by using dual‐beam time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS). The analysis was preceded by the following three steps: (1) determination of the optimal analytical conditions of the analysis beam (Bi+) and sputtering beam (Cs+), (2) verification of the etching methods to thin the SiO2 layer, and (3) confirmation of the benefits of the low‐energy sputtering beam directed toward SiO2/SiC samples. By using the secondary ion intensity peak‐to‐valley ratio of BN− and BO− of a sample with delta‐doped boron multilayers, the appropriate Bi+/Cs+ condition for a high depth resolution was determined for each energy level of the sputtering beam. Upon verification of the etching methods to thin the SiO2 layer, slight discrepancies were found between samples that were obtained with different etching methods. The difference in the roughness values of the etched surfaces was proactively utilized for the performance confirmation of the low‐energy sputtering beam by means of precise observation of the profiles at the SiO2/SiC interface. The use of a Cs beam with a low energy between 0.25 and 0.5 keV enabled the detection of slight discrepancies in the roughness of less than 1 nm between samples. The aforementioned method has the potential to accurately detect discrepancies in the intrinsic distribution at the SiO2/SiC interface among samples.