The work is devoted to modeling and verification of the dynamics of charged components of the Earth's lower ionosphere, obtained using different values of the background neutral atmosphere parameters. Long‐term experimental data on temperature and concentration of neutral components from the Aura satellite and Mass Spectrometer Incoherent Scatter Radar (MSIS) model were used as input data. The average relative difference between the electron concentration values obtained using Aura and MSIS data (11 June 2014, 6–18 UT, h = 50–90 km, 41°N 10°E) was 34%. Obtained results were verified with use of very low frequency (VLF) signals propagation data, which were collected on Mikhnevo Geophysical Observatory (GPO) and A118 station from GBZ, GQD, DHO, TBB, and ICV transmitters. Based on the results of the verification, it was found that the response of the lower ionosphere to X‐ray flares, that occurred on 9–11 June 2014, is better described by the Aura satellite data in 4 out of 5 cases. Consequently, they are more preferable for predicting the state of ionospheric parameters below the reflection height of signals of the considered frequencies (∼75 km). It is also shown that taking into account the ion concentration for calculation the amplitude‐phase characteristics of the VLF‐signals makes it possible to describe the dynamics of parameters better.