Long-lived metallic ions in the Earth's atmosphere (ionosphere) have been investigated for many decades. Although the seasonal variation in ionospheric “sporadic E” layers was first observed in the 1960s, the mechanism driving the variation remains a long-standing mystery. Here, we report a study of ionospheric irregularities using scintillation data from COSMIC satellites and identify a large-scale horizontal transport of long-lived metallic ions, combining the simulations of the Whole Atmosphere Community Climate Model with the chemistry of metals and ground-based observations from two meridional chains of stations from 1975–2016. We find that the lower thermospheric meridional circulation influences the meridional transport and seasonal variations of metallic ions within sporadic E layers. The winter-to-summer meridional velocity of ions is estimated to vary between −1.08 and 7.45 m/s at altitudes of 107–118 km between 10–60∘ N. Our results not only provide strong support for the lower thermospheric meridional circulation predicted by a whole atmosphere chemistry–climate model, but also emphasize the influences of this winter-to-summer circulation on the large-scale interhemispheric transport of composition in the thermosphere–ionosphere.