Ethnic minority medicinal plants (EMMPs) are an underutilized but critical resource for drug discovery; yet, face escalating threats from overharvesting and climate change. Here, we conduct the first comprehensive assessment of 5,820 EMMPs, evaluating their distribution, conservation status, and climate vulnerability to support global biodiversity goals. Key findings reveal distinct biogeographic patterns among ethnic minority medicinal clades, with southwest China harboring most biodiversity hotspots. Alarmingly, conservation effectiveness declines sharply at higher priority thresholds, leaving many critical habitats unprotected. Meanwhile, climate projections reveal severe range contractions for endemic and threatened EMMPs, even in traditional refugia like the Hengduan Mountains. Our study exposes urgent gaps in EMMP conservation and provides an evidence-based framework to prioritize protection efforts. These insights directly support the implementation of the “30 × 30” initiative, thus offering targeted strategies to safeguard this vital yet neglected component of biodiversity.