Abstract Low‐level clouds over the Southern Ocean (SO) exert a strong influence on surface radiation, yet their representation in reanalyses and climate models remains uncertain. We evaluated cloud properties and surface radiative fluxes from ERA5, MERRA‐2, and the CAM‐ATRAS model using observations obtained over the SO by Japan’s R/V Shirase during December 2022 and March 2023. ERA5 and MERRA‐2 overestimate the frequency of low‐level clouds with a base below 1 km. Although CAM‐ATRAS also overestimates very low clouds, it shows the best overall agreement with observations in cloud occurrence and phase. Despite the high frequency of low‐level clouds, all data sets underestimate downward longwave (DLW) radiation. Cold bias and cloud phase bias likely reduce cloud‐base emissivity and contribute to underestimated DLW radiation. Aerosol sensitivity experiments using CAM‐ATRAS indicate that enhanced cloud condensation nuclei concentrations increase low‐level cloud frequency but have a limited impact on surface radiative fluxes.