The thermodynamic structure of the lower troposphere in the 37 standard levels ERA5 reanalysis has been evaluated against 2,186 high‐resolution upper air soundings collected over the Southern Ocean (SO). The reanalysis, which incorporated these soundings, was found to be skilled in depicting the general synoptic meteorology and thermodynamic structure as defined by the cluster analysis of Truong et al. (2020) Journal of Geophysical Research: Atmospheres, 125, e2020JD033214. Using dew‐point depression as a proxy for cloud, however, we found a significant reduction in the number of inferred cloud layers, which is inherited from a bias in the specific humidity in the ERA5 reanalysis, most notably over the high latitudes of the SO, where a multilayer cloud structure is frequently observed. The reanalysis was also found to have thinner inferred cloud geometric layer and shallower cloud top heights. Further analysis showed that the reanalysis displays a greater percentage of soundings having no inversion with this bias being more pronounced at high latitudes that tends to be associated with the colder sea surface temperature. While the statistics of the main inversion height are largely consistent, the average inversion strength in the ERA5 reanalysis is found to be weaker than the observations. We anticipate the 137‐level ERA5 reanalysis simulation yields a smoothed vertical structure, from which the 37 standard levels ERA5 reanalysis is linearly interpolated. An examination of the sensitivity of the radiative transfer to cloud macrophysics suggests that the correct representation of thin multiple cloud layers can help reduce the amount of downward shortwave surface radiation over the SO.