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<p>In the previous work of Yue et al. (2022), the ionospheric evolution during the Holocene (9455 BC to 2015 AD) was comprehensively and carefully investigated for the first time using the Global Coupled Ionosphere-Thermosphere-Electrodynamics Model developed at the Institute of Geology and Geophysics, Chinese Academy of Sciences (GCITEM-IGGCAS), driven by realistic geomagnetic fields, <span class="inline-formula">CO₂</span> levels, and solar activity derived from ancient media records and modern measurements. In this study, we further quantify the effects of the three drivers on thermospheric neutral density and temperature variations during the Holocene. We find that the oscillations of solar activity contribute more than 80 % of the thermospheric variability, while either <span class="inline-formula">CO₂</span> or the geomagnetic field contributes less than 10 %. The effect of <span class="inline-formula">CO₂</span> on the global mean neutral density and temperature is comparable to that of the geomagnetic field throughout the Holocene but is more significant after 1800 AD. In addition, thermospheric density and temperature show approximately linear variations with the dipole moment of the geomagnetic field, <span class="inline-formula">CO₂</span>, and F10.7, with only the linear growth rate associated with the geomagnetic field varying significantly in universal time and latitude. The increasing dipole moment and <span class="inline-formula">CO₂</span> cool and contract the thermosphere, while solar activity has the opposite effect. The higher the altitude, the greater the influence of the three factors on the thermosphere. Different factors produce different seasonal variations in thermosphere changes. Furthermore, we predict that a 400 ppm increase in <span class="inline-formula">CO₂</span> will result in a 50 %–70 % and 84–114 K reduction in global mean neutral density and temperature, respectively, which should directly affect the orbit and lifetime of spacecraft and space debris.</p>