Pelagic fishes are a key trophic component of the Southern Ocean ecosystem; however, understanding the spatial and temporal changes in geographic distribution patterns of pelagic fishes in the context of climate change remains limited. To further support the development and refinement of biological management and conservation strategies for marine fishes in the Southern Ocean. This research applied the MaxEnt model to project the distributions of current and future (2100s) suitable habitats for ten major pelagic fish species in the Southern Ocean. Results suggested that the current spatial distribution of pelagic fishes is significantly correlated with their realized niche and that global warming will lead to significant changes in the spatial distribution of pelagic fishes in the Southern Ocean. Model predictions showed that eight out of ten pelagic fish species are likely to face a significant reduction in their ranges of suitable habitats under the RCP8.5 scenario by the 2100s. Except for the Bathylagus antarcticus, all of the other nine species were predicted to migrate toward South Pole by the 2100s. In addition, the community composition of pelagic fishes also may change significantly, mostly because of species loss. The results of this study clarify the impact of climate change on pelagic fishes in the Southern Ocean, and provide theoretical support for sustainable management and conservation efforts of these pelagic fishes.