Long-term trends in the tropospheric cosmic ray induced ionization on the multi-millennial time scale are studied using the newly released paleomagnetic reconstruction models. Spatial and temporal variations of the tropospheric ionization has been computed using the CRAC:CRII model and applying the paleomagnetic CALS7k.2 reconstruction. It has been shown that long-term variations of the tropospheric ionization are not spatially homogeneous, and they are defined not only by solar (i.e., covariant with solar irradiance) changes but also by the geomagnetic field. The dominance of the two effects is geographically separated, which makes it possible to distinguish between direct and indirect solar–terrestrial climate effects. Possible climate applications are considered.