AbstractThe exchange of energy between the lower atmosphere and the ionosphere thermosphere system is not well understood. One of the parameters that is important in the lower thermosphere is atomic oxygen. It has recently been observed that atomic oxygen is higher in summer at ∼95 km. In this study, we investigate the sensitivity of the upper thermosphere to lower thermospheric atomic oxygen using the Global Ionosphere Thermosphere Model (GITM). We use the Whole Atmosphere Community Climate Model with thermosphere and ionosphere extension (WACCM‐X) to drive the lower atmospheric boundary of atomic oxygen in GITM between ∼95 and 100 km and compare the results with the current mass spectrometer incoherent scatter (MSIS) driven GITM. MSIS has higher atomic oxygen in the winter hemisphere while WACCM‐X has higher atomic oxygen in the summer hemisphere. The reversal of atomic oxygen distribution affects the pressure distribution between 100 and 120 km, such that the hemisphere with larger O number density has stronger equatorward winds, and lower temperature mainly due to adiabatic and radiative cooling. This affects thermospheric scale heights such that the hemisphere with more O has lower N2 and thus enhanced O/N2. This behavior is observed in the opposite hemisphere when MSIS is used as the lower boundary for GITM. Overall, O/N2 for WACCM‐X driven GITM matches better with the global ultraviolet imager (GUVI) data. We find that the impact of lower thermospheric atomic oxygen on upper thermosphere is not just through diffusive equilibrium but also through secondary effects on winds and temperature.