Ammonia volatilized from penguin excreta is a significant nitrogen source in Antarctic ecosystems, influencing climate through new particle formation (NPF). Freeze-thaw events can trigger ammonia emissions, but their impact on penguin-derived ammonia is understudied and overlooked in models. Here we investigate the contribution of penguins to ammonia and their climatic impacts using cruise observations and GEOS-Chem-APM simulations. High ammonia concentrations, with a maximum exceeding 7000 ng/m³, were observed over the Southern Ocean and Prydz Bay, driven by air masses from penguin colonies. Simulations showed that incorporating freeze-thaw impact improves model performance, with penguin-derived ammonia emissions enhanced by up to 20-fold and reaching a total of 49 Gg across Antarctica in November. Elevated ammonia increased simulated secondary particle number concentrations by 30−300% through NPF, enhancing simulated cloud droplet number concentrations by 10−20% and altering cloud properties. This study underscores the importance of incorporating penguin emissions into models, particularly during freeze-thaw events.