In this study, we investigated the formation behavior of oxygen precipitates in Si wafers after a rapid thermal process (RTP) at 1350 °C in an oxygen atmosphere through experiments and simulations. The oxygen precipitate density varied based on the temperature (750–950 °C) and duration (0.5–16 h) of the first step of the two-step heat treatment after RTP. The highest oxygen precipitate density was achieved when the first-step temperature was set to 850 °C, and the second-step temperature was fixed at 1000 °C. The simulation consisted of the calculation of the depth profiles of the residual vacancy concentrations after RTP and oxygen precipitation during the two-step heat treatment after RTP. An empirical formula, in which the nucleation rate of the oxygen precipitates was assumed to be proportional to the fourth power of the residual vacancy concentration, was used in the temperature range of 600–1000 °C. In addition, we assumed that interstitial Si atoms, which were generated by the growth of the oxygen precipitates, consumed the residual vacancies through pair annihilation, thus stopping oxygen precipitation owing to the depletion of the residual vacancies. The simulation effectively reproduced the variations in the oxygen precipitate densities under different conditions in the first step of the heat treatment. Considering the results of the simulation, we concluded that the resulting oxygen precipitate density was determined by the nucleation rate, growth size, and timing of the terminal point of the nucleation.