The Southern Ocean (SO) is a unique region with rich ecosystems and minimal anthropogenic and terrestrial natural impacts especially during austral summer. We conducted measurements and sampling of aerosol particles to investigate the characteristics and role of aerosol particles in cloud formation on Japanese research vessel Mirai over the SO in the late austral summer of 2017. Observations of air masses with minimal terrestrial impacts indicated that bimodal aerosol particle size distributions were mostly observed over the SO and relative abundances of two modes varied with the changes in the structure of the marine boundary layer (MBL) such as surface mixing layer. As the local minimum diameter between two modes (DH) is considered a critical size for cloud‐droplet activation in the MBL, we analyzed the aerosol particles with diameter larger than DH (CNAcc) as a proxy for cloud condensation nuclei. Variations in the concentrations of aerosol particles with diameter larger than 300 nm were accounted for by the sea‐spray source function, whereas it substantially underestimated those of CNAcc. This implies the significance of the nonsea‐spray sources of CNAcc in the MBL over the SO. The concentrations of ice nucleating particles (NINPs) active at −25°C were 20–100 m−3, consistent with recent observations over the summertime SO. The observational evidence of very low NINPs relative to the CNAcc concentrations (40–110 cm−3) over a wide area of the SO is important for predicting the effects of cloud radiative properties on the radiative balances over the SO using climate models.