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The novel coronavirus pneumonia triggered by COVID-19 is now raging the whole world. As a rapid and reliable killing COVID-19 method in industry, electron beam irradiation can interact with virus molecules and destroy their activity. With the unexpected appearance and quickly spreading of the virus, it is urgently necessary to figure out the mechanism of electron beam irradiation on COVID-19. In this study, we establish a virus structure and molecule model based on the detected gene sequence of Wuhan patient, and calculate irradiated electron interaction with virus atoms via a Monte Carlo simulation that track each elastic and inelastic collision of all electrons. The characteristics of irradiation damage on COVID-19, atoms’ ionizations and electron energy losses are calculated and analyzed with regions. We simulate the different situations of incident electron energy for evaluating the influence of incident energy on virus damage. It is found that under the major protecting of an envelope protein layer, the inner RNA suffers the minimal damage. The damage for a ∼100-nm-diameter virus molecule is not always enhanced by irradiation energy monotonicity, for COVID-19, the irradiation electron energy of the strongest energy loss damage is 2 keV.