Waves in Earth’s atmosphere transfer energy and momentum into the ionosphere-thermosphere (IT) system, modulating winds, temperatures, and plasma distributions. These processes impact satellite drag, GPS signals, and radio communication. We compare two whole-atmosphere model simulations during September 2021: one using standard resolution, and another using a high-resolution configuration (HR-WACCM-X) that better resolves small-scale gravity waves and global-scale dynamics. The high-resolution model more accurately captures two key wave components active during this period: the non-migrating diurnal tide with zonal wavenumber 3 (DE3) and an approximately 3-day ultra-fast Kelvin wave. Unlike the coarse run, HR-WACCM-X reproduces realistic amplitudes, vertical structures, and spatiotemporal variability, including propagation into the F-region. Comparisons with ICON (thermospheric winds) and COSMIC-2 (electron density) confirm improved agreement above approximately 100 km. These results underscore the importance of resolving fine-scale gravity waves and nonlinear interactions in whole-atmosphere models to simulate day-to-day ionospheric variability. Enhancing model fidelity in this way improves our ability to predict upper atmospheric conditions and strengthens space weather forecasting.