Subterranean ecosystems harbor a high diversity of narrow-range endemics, yet they remain largely invisible in conservation planning, representing a major bias that may trigger irreversible biodiversity loss under rapid climate change. This study applied an Ensemble of Small Models (ESMs) framework, coupled with a target-group background strategy, to assess the climate vulnerability and protection status of Zopherobatrus Yin & Li, 2015 (Coleoptera: Staphylinidae: Pselaphinae), an extremely rare troglobitic rove beetle genus endemic to the karst landscapes of southwest China. Habitat suitability was projected under current conditions and across the 2050s and 2070s (SSP1-2.6 and SSP5-8.5). Under current conditions, highly suitable habitat is strictly confined to specific karst terrains; future projections reveal that the retained habitat ratio declines to only 24.0–48.2%, while the conventional net area change metric (–36.4% to –63.1%) masks functional habitat loss because climatically “gained” areas remain ecologically inaccessible to this dispersal-limited group, and the projected range centroid shifts northwestward by up to 141 km. A systematic gap analysis, cross-referenced with national and provincial nature reserves, showed that only 2.6% of current suitable habitat is formally protected, all known localities fall entirely outside reserves, and 95.9% of identified climate refugia lack any legal protection. These findings quantified a “double jeopardy” for subterranean biodiversity: simultaneous habitat erosion driven by climate change combined with a near-total absence of formal protection. The establishment of targeted micro-reserves centered on climate refugia, the formal inclusion of Zopherobatrus in national protection lists, and the integration of subterranean fauna into regional conservation frameworks are recommended.