The serious charging effect of polymer film with a thickness of the order of microns under the radiation of high-energy transmission electron beam, on the reliability of the micro-nano electronic device in electron microscopy detection is investigated. The charging effect of the polymer film is numerically calculated in this paper. The scattering process is simulated by the Monte Carlo method. The elastic scattering is calculated with the Rutherford scattering model. The inelastic scattering is simulated with the fast secondary electron (SE) model and the Penn model. The transport, the capture, and the recombination process of the charges are treated with the finite difference method. The fourth-order Runge-Kutta method is used to solve the trajectory of the emitted SEs. The dynamic distributions of the net charge, the built-in electric field, the surface emission current, and the transmission current are investigated, and the influence of the film thickness and the beam energy on the charging characteristics are analyzed. The results show that due to the emission of electrons near the sample surface, the distribution of the net charge in the sample is first positive and then negative along the incident direction. In addition, under the irradiation,higher charge quantity is deposited in the sample, and the net charge density increases gradually. However, with long-time irradiation, the deposited electrons transport to the surface under the action of built-in electric field which reduces the surface net charge density. Therefore the net charge density tends to a stable value. The space potential is positive in the surface and negative inside the sample. Therefore some emitted SEs return to the surface, resulting in the electron beam-induced current. With the irradiation, the positive surface potential increases and tends to a stable value. Hence the actual surface emission current decreases to a stable value and the sample current increases to a stable value. The sample current remains unchanged due to the weak charging strength. Increasing the film thickness leads the transient time to increase, which contributes to the decline of the surface potential and the increase of the actual emission currentand sample current. The increase of the beam energy causes the transmission current to increase and the sample current to decrease. In addition, it reduces the positive surface potential and the actual surface emission current accordingly. The results conduce to the decrease of the charging effect of the polymer film under the radiation of high-energy electron beam in the electron microscopy.