Based on photon transport theory and the theory of electron-semiconductor interactions, a model for the formation mechanism of gain noise caused by the secondary electron fluctuations in the electron multiplying layer of Electron Bombarded Complementary Metal-Oxide-Semiconductor (EBCMOS) devices is established. Using the Monte Carlo simulation method, the signal-to-noise ratio (SNR) of secondary electrons is calculated, with a focus on analyzing the impact of system parameters, including incident electron energy, passivation layer type and thickness, electron multiplying layer thickness, and doping concentration, on gain noise. The results indicate that by using Al2O3 as the passivation layer material, and implementing a series of measures such as reducing passivation layer thickness, lowering doping concentration, decreasing electron multiplying layer thickness, and lowering operating temperature, the SNR of the electron multiplying layer can be effectively improved to 75.35 dB. The findings of this study provide theoretical guidance for the preparation of the EBCMOS electron multiplying layer.