Numerical modeling of primary cosmic ray protons’ transport through the Earth’s atmosphere was performed for the energy spectra of solar energetic particle events (SEPs). Several events in the last three solar cycles were considered. A comparative analysis of the characteristics of coronal mass ejections and primary proton fluxes was carried out. The main results were quantitative estimates of the calculated atmospheric ionization count rate for a wide range of altitudes (from sea level up to 98 km). The difference in the influence of solar protons on the Earth’s atmosphere is considered for seven SEPs divided into three groups with similar solar sources (X-flare magnitude and coordinates) but with different characteristics of accelerated particle fluxes. The data obtained in this work are very important for future studies of radio wave propagation, atmospheric chemistry and climate change.