In this paper, various surface structures of electron multiplier layer are designed, and the influence of doping distribution on the charge collection efficiency of electron bombardment CMOS (EBCMOS) imaging device is simulated and analyzed. Combined with ion implantation process, the surface structure of electron multiplier layer was optimized, and the influence of different kinds and thickness of masking layer, ion implantation dose, implantation angle and implantation times on doping distribution was analyzed by using ion implantation simulation software TRIM. According to the carrier transport theory and Monte Carlo simulation method, the charge collection efficiency of electron multiplier layer in EBCMOS is simulated and analyzed. The simulation results show that the charge collection efficiency can be improved by selecting SiO2 as the masking layer, reducing the thickness of the masking layer and increasing the number of energy injection. In the aspect of injection dose selection, heavily doping the surface layer of the electron multiplication layer can make the doping concentration decrease large enough and slow enough, which can also effectively improve the charge collection efficiency. After optimization, the charge collection efficiency of the device corresponding to the surface structure can reach 93.61%.