The Qinghai-Tibet Plateau (QTP) hosts rich and unique diversity of amphibians and reptiles, which are vulnerable to climate change and anthropogenic pressures. Despite recent protected area (PA) reforms and national park establishment, significant conservation gaps remain, especially in high species richness and endemic regions of amphibians and reptiles. To improve amphibian and reptile conservation on the QTP, we assessed the effectiveness of the current PA systems under both current and future climate scenarios, using ensemble species distribution models (SDMs) covering 94.77 % of amphibian and 98.43 % of reptile of distributed species, which is the first plateau-wide SDM ensemble for >95 % (96.69 %) of the herpetofauna. We introduced the Conservation Necessity Index (CNI), a novel framework integrating species rarity with threat status, to systematically prioritize conservation areas for amphibians and reptiles across the QTP. We identified critical gaps in the existing PA systems, within the Nujiang, Lancang, Jinsha, and Min river basins, and particularly in the Yarlung Tsangpo river basin in the southern Himalayas. Under future climate scenarios, high-richness regions could contract by 14–30 %, disproportionately affecting narrow-range endemics, which underscores the urgency of adaptive conservation planning. We propose targeted PA expansions, dynamic management, and community-based strategies to enhance climate resilience.