<p>Antarctic krill (<i>Euphausia superba</i>) and salps (<i>Salpa thompsoni</i>) are vital and important macrozooplankton grazers in the Southern Ocean ecosystem. However, the impact of climate change on their habitats remains unclear, particularly regarding the potential spatial displacement of krill habitats due to the southward expansion of salps. Understanding the interactions between these two key species in the Southern Ocean ecosystem is therefore crucial. This study used ecological niche modeling to predict the austral summer and autumn habitat distribution and ecological niches of krill and salps during the period (1996–2015) and under future scenarios (2050s and 2100s). The results showed that krill are mainly distributed in shelf regions, while salps are more prevalent in open ocean areas farther north compared to krill, such as the Lazarev Sea. Additionally, some overlap in their distributions is observed in the Western Antarctic Peninsula, the Kerguelen Islands and the Ross Sea. Under future scenarios, both krill and salps are projected to experience a reduction in their high-potential habitats, with decreasing spatial and ecological overlap. This study emphasizes the significance of krill and salps interactions in the Southern Ocean ecosystem. The findings provide valuable information for the conservation and management of the Southern Ocean ecosystem.</p>