Recent high‐resolution dropsonde observations from the 2010 Concordiasi field campaign in austral spring season show that surface‐based inversions ( SBIs ) over Antarctica are frequently eroded, with well‐mixed boundary layers occurring 33% and 18% of the time in West and East Antarctica, respectively. In this study, using the dropsonde observations, we evaluate the performance of the Modern‐Era Retrospective analysis for Research and Applications, version 2 (MERRA2) in representing the Antarctic boundary layer thermodynamic structure. Results show that MERRA2 has a good overall representation of the Antarctic surface stability and correctly predicts 82% of the SBIs . However, an underprediction of less stable boundary layer occurrence, especially over the elevated East Antarctic plateau, is favored during conditions of increased lower tropospheric stability associated with model dynamics, indicating difficulty in parameterizing turbulence in very stable boundary layers. In addition, a lower tropospheric cool bias (first model level and above) is observed in the MERRA2 reanalysis, especially over West Antarctica, which amplifies in the boundary layer during mixed conditions. The near‐surface cold bias is most pronounced when the model fails to predict mixed layers over West Antarctica and is expected to negatively impact the representation of surface energy budget and melt processes.