Electron density profiles of the ionosphere of Mars derived from radio occultation data obtained by the radio science Mars Global Surveyor (MGS) experiment have been compared with the crustal magnetic fields measured by the MGS Magnetometer/Electron Reflectometer (MAG/ER) experiment. In the northern hemisphere the crustal fields are rather weak and usually do not prevent direct interaction between the solar wind (SW) and the Martian ionosphere/atmosphere. Exceptions do occur in the isolated mini-magnetospheres formed by the crustal anomalies. Much stronger crustal fields are located in limited regions in the southern hemisphere and lead to the formation of large-scale mini-magnetospheres. A study of the electron density profiles obtained when the mini-magnetosphere regions are near the terminator has been conducted using the magnetic field measurements at altitudes 170--180 km and 400 km. The magnitude of the electron density peak and the effective scale-height of the electron density for two altitude ranges, 145--165 km and 165--185 km, have been derived for each of the 326 selected profiles studied. In each hemisphere, the longitudinal variations of these derived parameters have been studied. A significant difference between the large-scale mini-magnetospheres and regions outside of them has been found. The neutral atmosphere is cooler inside the large-scale mini-magnetospheres. The variations of the magnitude of the electron density peak indicate that the electrons are usually hotter inside a large-scale mini-magnetosphere than outside. It appears that the mini-magnetospheres formed by strong crustal magnetic fields prevent additional heating of the neutral atmosphere due to direct interaction of the SW and also confine the hotter electrons created by photo ionization.