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<p>On timescales longer than the solar cycle, long-term changes in CO<span class="inline-formula">₂</span> concentration and geomagnetic field have the potential to affect thermospheric dynamics. In this paper, we investigate the thermospheric dynamical response to these two factors during the Holocene, using two sets of <span class="inline-formula">∼12 000</span>-year control runs by the coupled thermosphere–ionosphere model, GCITEM-IGGCAS. The main results indicate that increased/decreased CO<span class="inline-formula">₂</span> will enhance/weaken the thermospheric circulation throughout the Holocene, but this effect is non-linear. The cooling effect of CO<span class="inline-formula">₂</span> in the thermosphere further provides plausible conditions for atmospheric tidal propagation and increases the thermospheric tidal amplitude. Geomagnetic variations induce hemispheric asymmetrical responses in the thermospheric circulation. Large changes in the circulation occur at high latitudes in the hemisphere with distant magnetic pole drift, inferring a crucial role of geomagnetic non-dipole variations in circulation changes. A positive correlation between the diurnal migrating tide (DW1) and geomagnetic dipole moment is revealed for the first time. The amplitude of DW1 in temperature will increase by <span class="inline-formula">∼1</span>–3 K for each <span class="inline-formula">1×10²²</span> A m<span class="inline-formula">²</span> increase in dipole moment.</p>