Global climate models (GCMs) are challenged by difficulties in simulating cloud phase and cloud radiative effect over the Southern Ocean (SO). Some of the new-generation GCMs predict too much liquid and too little ice in mixed-phase clouds. This misrepresentation of cloud phase in GCMs results in weaker negative cloud feedback over the SO and a higher climate sensitivity. Based on a model comparison with observational data obtained during the Southern Ocean Cloud Radiation and Aerosol Transport Experimental Study, this study addresses a key uncertainty in the Community Earth System Model version 2 (CESM2) related to cloud phase, namely ice formation in pristine remote SO clouds. It is found that sea spray organic aerosols (SSOAs) are the most important type of ice nucleating particles (INPs) over the SO with concentrations 1 order of magnitude higher than those of dust INPs based on measurements and CESM2 simulations. Secondary ice production (SIP) which includes riming splintering, rain droplet shattering, and ice-ice collisional fragmentation as implemented in CESM2 is the dominant ice production process in moderately cold clouds with cloud temperatures greater than −20°C. SIP enhances the in-cloud ice number concentrations (Ni) by 1–3 orders of magnitude and predicts more mixed-phase (with percentage occurrence increased from 15% to 21%), in better agreement with the observations. This study highlights the importance of accurately representing the cloud phase over the pristine remote SO by considering the ice nucleation of SSOA and SIP processes, which are currently missing in most GCM cloud microphysics parameterizations.