As a key component, CCD has been widely used in space-based CCD cameras. However, it is vulnerable to the impact of high-energy electron radiation in space environment, resulting in performance degradation and abnormal operation. For this problem, a domestic N-channel three-phase polysilicon CCD with an overlapping gate and frame-transfer structure is selected to study the effect of electron irradiation. The models were established by FLUKA for Si and SiO₂ irradiated with electrons, which are the composition material of CCD. We simulated the physical process of electrons and material interaction and calculated the total mass stopping power and range of different energy electron beams in Si and SiO₂, then compared them with the theoretical results, and the correctness of the simulation method is verfied. A three-dimensional model of CCD pixel array was established. The effects of electron irradiation with different energy on the energy deposition process of electrons in CCD and the effect of between pixels on DPA (Displacement Per Atom) of electrons in CCD pixels were simulated and calculated. The mechanism of radiation damage difference is analyzed respectively.