The electron beam deposition process of SiO2 thin film with large angle and wide aperture is dominated by self-shadowing effect, which deviates from the traditional thickness distribution model. In this paper we develop a modified model based on the traditional one and calculate the SiO2 relative thickness distribution in consideration of the self-shadowing effect. The deviations between the modified theoretical model and experimental data are largely reduced compared to that between the classical theory and experimental data. In comparison with the classical model, the mean deviation of the relative film thickness is reduced by 1.91%, the maximum deviation of the relative film thickness is decreased by 2.38%, and the root mean square deviation of the relative film thickness is reduced by 2.05% in comparison with the classical model, suggesting that this modified model is more accurate in describing the large angle and wide aperture deposition situations than the classical one. This study may provide a new way to modify the deposition thickness distribution under similar conditions.