With regard to Secondary Ion Mass Spectroscopy (SIMS) measurement of atmospheric gas elements, a problem occurs that the detected signal includes background components caused by residual gas along with contained components. Relating to this issue, an available method to quantify the contained components by separating the background ones had been established for Dynamic SIMS. Time‐of‐Flight SIMS with sputtering ion gun has also applied for depth profiling as well as Dynamic SIMS. However, few studies have attempted to investigate the secondary ion behavior of the atmospheric gas elements for depth profiling by Time‐of‐flight SIMS, especially for low concentration levels. In this study, experimental examinations of the secondary ions of the atmospheric gas elements, such as oxygen, hydrogen, and carbon in the silicon substrate, has been conducted in various analytical conditions of TOF‐SIMS depth profiling mode. Under the analytical conditions of our study, it has been proved that the background intensity of these elements was correlated to the sputtering rate. For the analysis of Floating Zone Silicon substrate, the oxygen intensity of the background component was proportional to the inverse number of the sputtering rate. Based on these facts, the total detected intensity of the atmospheric gas elements was able to be separated into the contained components and background ones by changing the sputtering rate during TOF‐SIMS measurement. An experimental result has shown that the contained oxygen concentration in the Czochralsk Silicon substrate estimated by the “TOF‐SIMS Raster Change Method” has successfully agreed with the result by the Dynamic SIMS.