Biodiversity conservation is critical for maintaining ecosystem integrity in species-rich regions like North-East India (NEI), a key part of the Indo-Burma biodiversity hotspot. NEI supports a diverse assemblage of 269 mammal species, including 48 threatened and 13 endemic species, yet faces escalating habitat loss and fragmentation from anthropogenic pressures. This study presents a novel framework for identifying spatial conservation priorities and ecological refuges specifically within the Mizo and Cachar Hills, which retain critical interior forest patches indispensable for arboreal and range-restricted fauna. Utilizing Area of Habitat (AOH) data for 240 species, we integrated functional richness with a Regional Conservation Priority Index (RCPI) that weights IUCN threat status, regional endemism, and range restriction. Our analysis separately evaluates large-bodied (>10 kg) and small-bodied (≤10 kg) mammals to ensure top-down and bottom-up ecological processes are preserved. Using Morphological Spatial Pattern Analysis (MSPA), we identified intact core habitat zones characterized by stable environmental conditions insulated from edge effects. A composite Conservation Score Map (CSM) identifies eight landscapes for large mammals and four for small mammals as high-priority zones. Results indicate that over 30% of NEI’s land is of high conservation value, yet nearly 90% of these priority zones lie outside the existing Protected Area (PA) network. This data-driven approach supports evidence-based policymaking and aligns with global targets, such as the Kunming–Montreal Framework’s 30 × 30 goal, by providing a scientific basis for expanding PAs and communitymanaged conservation areas.