Loud noise due to sonic boom is strongly affected by atmospheric conditions such as humidity, temperature, and wind including velocity fluctuation in the atmospheric boundary layer. In this study, we simulated the atmospheric conditions for the past 10-years based on historical meteorological data, and the sonic boom of the pseudo-Concorde and the Low-Boom Concept (LBC) models along the flight routes were numerically investigated under the simulated atmospheric conditions. The results show that the overpressure of a sonic boom pressure signature varies seasonally, and the overpressure decreases in winter. Molecular relaxation due to atmospheric humidity affects mainly pressure attenuation; however, the overpressure of the LBC is less sensitive to the atmospheric variation than that of the pseudo-Concorde.