Atmospheric neutrons can cause the single event effect (SEE) of integrated circuits, resulting in data loss or functional interrupt. The SEE failure rate caused by atmospheric neutrons depends on its flux, thus obtaining the atmospheric neutron flux is the premise of SEE failure rate assessment. In this paper, the atmospheric neutron energy spectra and fluxes in Guangzhou, Lanzhou and Lhasa are measured using the Bonner sphere spectrometers (BSS). Typical characteristics of atmospheric neutron spectrum are obtained. The measured results show that the atmospheric neutron flux in different areas is affected by the altitude, and the terrestrial atmospheric neutron flux increases with the altitude. In addition, the nuclear reaction process of primary cosmic ray particles in the earth’s atmosphere can also be simulated based on the Monte Carlo simulation tools, so as to calculate the atmospheric neutron spectrum. It shows that the measured data of atmospheric neutron spectra are in good agreement with the simulation data. These data can be used in quantitative evaluation of atmospheric neutron-induced SEE of integrated circuits.