Gymnosia orchidis (G. orchidis) is a valuable Tibetan medicinal resource with significant medicinal, ecological, and economic value. However, the growth of G. orchidis is severely constrained by stringent natural conditions, leading to a drastic decline in its resources. Therefore, it is crucial to study the suitable habitat areas of G. orchidis to facilitate future artificial cultivation and maintain ecological balance. In this study, we investigated the suitable zones of G. orchidis based on 79 occurrence points in the Qinghai-Tibet Plateau (QTP) and 23 major environmental variables, including climate, topography, and soil type. We employed the Maximum Entropy model (MaxEnt) to simulate and predict the spatial distribution and configuration changes of G. orchidis during different time periods, including the last inter-glacial (LIG), the last glacial Maximum (LGM), the Mid-Holocene (MH), the present, and future scenarios (2041—2060 and 2061—2080) under three different climate scenarios (SSP126, SSP370, and SSP585). Our results indicated that annual precipitation (Bio12, 613—2466 mm) and mean temperature of the coldest quarter (Bio11, -5.8—8.5 °C) were the primary factors influencing the suitable habitat of G. orchidis, with a cumulative contribution of 78.5%. The precipitation and temperature during the driest season had the most significant overall impact. Under current climate conditions, the suitable areas of G. orchidis covered approximately 63.72×104/km², encompassing Yunnan, Gansu, Sichuan, and parts of Xizang provinces, with the highest suitability observed in the Hengduan, Yunlin, and Himalayan mountain regions. In the past, the suitable area of G. orchidis experienced significant changes during the Mid-Holocene, including variations in total area and centroid migration direction. In future scenarios, the suitable habitat of G. orchidis is projected to expand significantly under SSP370 (30.33%—46.19%), followed by SSP585 (1.41%—22.3%), while contraction is expected under SSP126. Moreover, the centroids of suitable areas exhibited multidirectional movement, with the most extensive displacement observed under SSP585 (100.38 km²). This research provides valuable insights for guiding the selection of introduced species, artificial cultivation, and resource conservation in the future, while also offering theoretical support for the protection of endangered species.