The charging of the polymer thin film irradiated by penetrating electron beam (e‐beam) is investigated, in parallel with the numerical simulation and experiment. The simulation is performed by combining scattering, drift, diffusion, trapping and recombination. Results show that, due to the electron emission the net charge near the surface is distribution positively, but negatively inside the film because of low electron mobility. The surface potential is positive near surface and accordingly forces some of secondary electrons to return surface. As irradiation proceeds, currents flowing into and out of the film can tend to equilibrium. In the equilibrium state, with increasing beam energy, the surface potential and the efficient emission current decrease, and the electron beam‐induced current and the transmission current tend to zero and the beam current valuable, respectively. E‐beams of 10‐30 keV cause positive charging on PMMA film of 2 µm, which means the high‐energy e‐beam can effectively discharge a thin film that has been charged negatively by irradiation with low‐energy e‐beam. With the increase of the film thickness from 1 to 3 µm, the positive surface potential and the emission current decreases and increases, respectively, and the transmission current tends to zero.