The SARS-CoV-2 virus is deadly, contagious, can cause COVID-19 disease, and endangers public health and safety. The development of SARS-CoV-2 inactivation technology is crucial and imminent in current pandemic period. Neutron radiation is usually used to sterilize viruses because neutron radiation is 10 times more effective than gamma-rays in inactivating viruses. In this work we established a closed SARS-CoV-2 inactivation container model by the Monte Carlo method and simulated the inactivation performance by using several different neutrons sources. To study the effects of inactivation container factors, including the reflector thickness, the type of the reflector material, the SARS-CoV-2 layer area and the distance from the radiation source on the energy deposition of a single neutron particle in SARS-CoV-2 sample, we simulated the neutron energy deposition on a SARS-CoV-2 sample. The simulation results indicate that the saturated thicknesses of reflector materials for graphite, water and paraffin are approximately 30 cm, 15 cm, and 10 cm, respectively, and the energy deposition (radiation dose) becomes larger when the SARS-CoV-2 layer area is smaller and the SARS-CoV-2 layer is placed closer to the neutron source. The calculated single-neutron energy deposition on 10 × 10 cm² SARS-CoV-2 layer is about 3.0059 × 10⁻⁴ MeV/g with graphite as the reflection layer, when the 14 MeV neutron source intensity is 10¹² n/s and the SARS-CoV-2 layer is 5 cm away from the neutron source. If the lethal dose of SARS-CoV-2 is assumed as the IAEA recommended reference dose, 25 kGy, the SARS-CoV-2 could be decontaminated in about 87 min, and the sterilization time could be less than 52 s if the 14 MeV neutron intensity is increased to 10¹⁴ n/s.