Antarctic krill (Euphausia superba), a key species in the Southern Ocean that supports a distinct food web and a valuable commercial fishery, faces a major threat from climate change. This study used an ensemble species distribution modeling framework, combined with the latest CMIP6 SSP4.5 and SSP8.5 climate scenarios, to forecast changes in suitable habitat for Antarctic krill in the 2050s and 2100s. Importantly, the analysis goes beyond traditional area-based methods by systematically applying a range of landscape ecology metrics to measure future changes in habitat spatial arrangement—specifically fragmentation and isolation. Projections indicate a significant southward shift and overall loss of suitable habitat by 2100, with reductions of 25.6% under SSP4.5 and 38.6% under SSP8.5. Landscape analysis identified two different degradation paths: an "active fragmentation" pattern under SSP4.5, where habitat becomes divided into more complex patches, and a "severe attrition and isolation" pattern under SSP8.5, marked by extensive habitat loss resulting in fewer, highly isolated patches. These shifts threaten population connectivity and resilience. Mean annual water temperature and silicate concentration were the two most important environmental factors. This work offers the first basin-scale, quantitative assessment of future habitat spatial configuration decline for Antarctic krill, highlighting the urgent need for climate-adaptive management. This includes creating dynamic fisheries management plans and establishing a climate-resilient network of Marine Protected Areas to protect this vital species and the broader Southern Ocean ecosystem.