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Charging effects caused by secondary electron (SE) emission near a 100-nm-high SiO2 step on a Si substrate are investigated. The system was irradiated by a 1-keV electron beam. We modeled SE emission by performing dynamic and self-consistent calculations of electron transport inside and outside the system. The model accounts for the electric field generated by positive and negative charges in the SiO2 step. Positive charging of the SiO2 step reduces the total electron yield to unity during irradiation. When the irradiation position is moved close to the edge of the step, charging decreases strongly and the electron yield increases sharply due to additional SE emission from the side wall of the step. When the Si substrate is irradiated with the electron beam, many SEs re-enter the side wall of the SiO2 step so that the wall surface becomes negatively charged. This negative charging deters other SEs from re-entering the step. Consequently, the reduction in the total electron yield of the Si substrate near the wall is more localized than that without charging.