Atmospheric perturbations induce different ionospheric states from one day to the next, and this weather-like phenomenon is known as day-to-day variability. Increased greenhouse gas (GHG) emissions are known to cause changes throughout the atmosphere, from the weather and climate system in the lower atmosphere to the global-scale state in the upper atmosphere. However, it is still unclear whether rising GHG concentrations influence the “ionospheric weather”. In this study, we explore the link between GHG and ionospheric day-to-day variability, using simulations of Whole Atmosphere Community Climate Model with thermosphere and ionosphere eXtension (WACCM-X). We performed ten sets of time-slice simulations with realistic GHG emissions, one set per decade from 1921–1925 to 2011–2015. Further ten sets of simulations excluded the secular variation of geomagnetic fields, the crucial factor in controlling ionospheric morphology. Our main results reveal significant trends in ionospheric day-to-day variability, with increasing GHG dominating the trends over the Asia-Pacific region. Additionally, Wuhan ionosonde observations spanning 1947–2025 corroborate the simulated trends. Analysis of atmospheric tides further suggests that the declining day-to-day variability in semidiurnal tides (SE2) should be a plausible cause. In summary, our work reveals a potential relationship between global climate change and the “ionospheric weather”.