Abstract The relative column abundance of monatomic oxygen to molecular nitrogen (ΣO/N 2 ) in the lower thermosphere has been measured for over two decades by TIMED/GUVI. This data set provides an opportunity to assess how well current empirical thermosphere climatologies reproduce observed composition variations on timescales of days to a solar cycle. Here, we characterize and compare the primary modes of daily mean thermospheric ΣO/N 2 variability measured by TIMED/GUVI and generated from NRLMSIS 2.0 over a solar cycle from 2008 to 2019 using principal component analysis. The geophysical significance of these modes and their dependence on solar and geomagnetic drivers is further determined. We find that the ΣO/N 2 variability over this period observed by GUVI is dominated by three distinct modes; two associated with intra‐annual variations, that is, the annual and semiannual oscillations (AO and SAO), and one associated with the response to geomagnetic activity. These three modes account for 88% of the total global variability over the time period; the AO accounts for 53%, the SAO accounts for 28%, and geomagnetic activity response accounts for 7%. The separation of the AO and SAO denotes unique spatial structures and driver modulation for each of these modes. NRLMSIS 2.0 shows strong agreement with GUVI for the geomagnetic activity mode. In contrast, the two modes associated with intra‐annual variations displayed different spatial structures and dependencies on solar‐geomagnetic conditions, particularly solar EUV radiative flux, compared to GUVI. These results highlight important discrepancies in intra‐annual variations of composition in the lower thermosphere between the NRLMSIS climatology and long‐term GUVI observations.