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In this study, we simulated the electron density disturbance at night in the bottom of the ionosphere caused by the electrostatic field in a thundercloud. The simulation was conducted using the charge of the thundercloud as the source, by incorporating a more up-to-date conductivity profile, and using the ion chemistry model for the lower ionosphere. The results revealed that a thundercloud charge of 30–100 C can cause a disturbance in the electron density in the lower ionosphere, decreasing to 40% of the original value or increasing to 160% of the original value. The electron density disturbance occurs mainly below an altitude of 80 km, and its peak is located at an altitude of 70 km, with a regional horizontal radius of about 50–75 km. The simulation results of this study improve the theory of Salem et al and extend the original one-dimensional model to three-dimensional space.