Background: The total yields of direct Single-Strand Breaks (SSBs) and Double-Strand Breaks (DSBs) in proton energies varying from 0.1 to 40 MeV were calculated. While other studies in this field have not used protons with energy less than 0.5 MeV, our results show interesting and complicated behavior of these protons. Materials and Methods: The simulation has been done using the Geant4-DNA toolkit. An atomic model of DNA geometry was simulated. Simulations were performed with a source in the Z-axis direction at the cell nucleus entrance with protons at energies of 0.1-1 MeV in 0.1 MeV steps, 5 MeV, and 10-40 MeV in 10 MeV steps. Results: The calculated SSB yields decreased from 60.08 (GbpGy)⁻¹ for 0.1 MeV proton energy to 49.52 (GbpGy)⁻¹ for 0.5 MeV proton energy, and then it increased to 54.35 (GbpGy)⁻¹ in 40 MeV. The DSB yields decreased from 4.32 (GbpGy)⁻¹ for 0.1 MeV proton energy to 1.03 (GbpGy)⁻¹ for 40-MeV protons. The DSB yields for energies less than 0.5 MeV was about 56%, and for the other energy levels, it was 44%. As for SSB yields, 35% of the breaks arose from protons with an energy of fewer than 0.5 MeV and 65% from higher energies. Conclusion: It was found that the proton ranges with an energy less than 0.5 MeV are smaller than the cell size (10 μm), and 100% of the energy is deposited in the cell region. Then protons with these energies are the best choice to increase the number of DSBs.