The Southern Ocean is a region of critical ecological importance, yet it faces compounding threats from climate change and human activities. Marine protected areas (MPAs) are essential spatial management tools to conserve biodiversity and mitigate these threats. However, progress in designating a representative MPA network in the Southern Ocean has recently stalled due to geopolitical deadlocks. This study utilizes bibliometric network analysis (CiteSpace and VOSviewer) to quantitatively evaluate 1899 global scientific literature concerning Southern Ocean MPAs, aiming to diagnose the health of underlying science-policy interface. The results reveal a significant publication surge corresponding to establishment of the South Orkney Islands Southern Shelf (2009) and the Ross Sea region (2016) MPAs. However, international collaboration exhibits a deeply entrenched core-periphery structure dominated by traditional polar nations, potential hindering consensus building within international governance frameworks. Thematic evolution analysis identifies a distinct transition in research focus, from initial paleoclimate baselines (1991–2009), through multi-disciplinary ecological integration (2010–2015), to the current frontier of MPA governance and policy frameworks (2015–present). To overcome negotiation bottlenecks, future Southern Ocean MPA research must bridge the critical gap between classical ecology and fisheries socio-economics, transition toward climate-driven dynamic spatial management, and foster inclusive, cross disciplinary collaborations that align with international frameworks such as the BBNJ Agreement.