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We examine impacts of geomagnetic activity (GA) on CO2‐driven trend in the ionosphere and thermosphere using the Ground‐to‐topside Atmosphere Ionosphere model for Aeronomy whole atmosphere model. The model reveals three salient features. (1) Geomagnetic activities usually weakens the CO2‐driven trend at a fixed altitude. Among the IT parameters analyzed, the thermosphere mass density is the most robust indicator for CO2cooling effect even with GA influences. (2) Geomagnetic activities can either strengthen or weaken the CO2‐driven trend in hmF2 and NmF2, depending on local time and latitudes. This renders the widely used linear fitting methods invalid for removing geomagnetic effects from observations. (3) An interdependency exists between the efficiency of CO2forcing and geomagnetic forcing, with the former enhances at lower GA level, while the latter enhances at higher CO2concentration. This could imply that the CO2‐driven trend would accelerate in periods of declining GA, while magnetic storms may have larger space weather impacts in the future with increasing CO2. These findings provide a preliminary model framework to understand interactions between the CO2forcing from below and the geomagnetic forcing from above. Geomagnetic activities usually weakens the CO2‐driven trend at a fixed altitudeGeomagnetic activities can either strengthen or weaken the CO2‐driven trend in hmF2 and NmF2, depending on local time and latitudesAn interdependency exists between the efficiency of CO2forcing and geomagnetic activity forcing Geomagnetic activities usually weakens the CO2‐driven trend at a fixed altitude Geomagnetic activities can either strengthen or weaken the CO2‐driven trend in hmF2 and NmF2, depending on local time and latitudes An interdependency exists between the efficiency of CO2forcing and geomagnetic activity forcing