Cathaya argyrophylla Chun et Kuang is an endangered relict gymnosperm endemic to China. Its habitat has been severely fragmented due to Quaternary glaciations, a condition further exacerbated by modern, fragmented administrative management. We compiled 98 spatially filtered occurrence records across four provinces and developed a combined analysis framework integrating the Biomod2 ensemble model with the Marxan systematic planning algorithm. Our optimal model (TSS = 0.911, AUC = 0.986) identified mean diurnal range and ultraviolet-B seasonality radiation as the dominant ecophysiological drivers of the species’ distribution. Currently, suitable habitats cover 7.10% of the study area, with highly suitable habitats accounting for only 3.08% (21.76 × 103 km2). Priority conservation areas account for 2.48% (17.55 × 103 km2) of the total area. A gap analysis revealed that 76.98% (13.51 × 103 km2) of the optimized priority conservation areas currently lack formal protection under China’s protected area system and the World Database on Protected Areas. Under four future climate scenarios (2030s–2090s), projections indicated overall habitat contraction, with limited spatial expansion observed only under specific scenarios (SSP1-2.6 in the 2030s and 2090s; SSP5-8.5 in the 2030s), and the population centroid was projected to shift southeastward by an average of 42.67 km in Huaihua City. Twenty-one core habitat patches were identified under current climate conditions. As these core habitat patches are concentrated along interprovincial boundaries, specifically the Dalou Mountains and the Yuecheng Ridge, our findings emphasize the need to bridge local administrative barriers. This spatial framework provides actionable guidelines for establishing transboundary protected areas, optimizing in situ conservation networks, and implementing model-based assisted migration.
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