Using the natural environment and socio-economic data on the Qilian Mountains, China, we selected 30 indicators and constructed an ecological redline evaluation index system based on three key aspects:ecosystem resilience, ecological sensitivity, and socio-economic influence. This system was constructed based on a GIS platform and a weighted sum multi-index computing model, so that it was possible to investigate ecological protection developments in the Qilian Mountains. Results showed that the ecological redline, yellow line, and green line zones accounted for 32%, 40%, and 28% of the total zone, respectively. The ecological redline zone is mainly located in the southwestern part of the Qilian Mountains, southern Tuolai Mountains, Qinghai Lake, and regions covered by glaciers, where the strictest controls should be implemented by the government. The ecological yellow line zone, characterized by the largest distribution area, mainly occurs in the middle and west Qilian Mountains, the middle reaches of the Huangshui Valley, and the southern part of the Wushaoling Mountains, where ecological restoration and the impact of agricultural land should be given priority. The ecological green line zone is mainly dominated by the eastern part of the Shulenan Mountains, where protection should be given priority in terms of providing ecological products and developing ethical ecological tourism by the regional government.