The negative charging process and its mechanism caused by low-energy electron beam (e-beam) irradiation have been clarified for an insulating thin film with a grounded conductive substrate. Numerical simulation is performed by considering both electron scattering and electron transport, in combination with the Monte Carlo method and the finite difference method. The internal space charge, leakage current, surface potential and their time-evolution under e-beam irradiation are eventually obtained under different e-beam conditions and for different SiO2 film parameters. Results show that owing to the drift produced by mobility and diffusion, incident electrons can go beyond the conventional scattering region and arrive at the substrate after a certain transit time, forming negative space charge and leakage current. The transient negative charging process tends to equilibrium as the leakage current increases. In the equilibrium state, the leakage current increases with the energy and intensity of the e-beam. Meanwhile, the amount of net negative charge and the absolute value of surface potential increase with the film thickness, decrease with the increase of electron mobility, and both exhibit a maximum value with variation of the e-beam energy.