Qilian mountain is one of the most famous twelve mountain chains in China and the most important ecological security barrier and the energy channel in northwest China. The ecological safety threshold value of the Qilian Mountain region is small due to its typical compound ecological system and fragile and sensitive characteristics. The ecological destruction problem in partial region of Qilian Mountain has been very serious for a long time because of its rich mineral resources. Related human activities such as deforestation，mining，etc has never stopped. The illegal mining，illegal construction of water and electricity facilities，illegal discharge of waste water and other wastes have been seen more and more in recent years. even if the successive establishment of the Qilian Mountain National Nature Reserve and the Qilian Mountain National Park failed to curb the situation. Comrade Xi Jinping have successively made important instructions on the ecological environment governance of Qilian Mountain from 2016 to 2017，the miserable condition of Qilian Mountain has been exposed to the public many times by media and exposed to the general information，also investigated for responsibility of related personnel. More and more attention has been given to the ecological protection of the Qilian Mountain，some environmental governance achievements have been obtained，the protection and restoration of the ecological system of the Qilian Mountain including hills，water，forest，field，lake and grassland have become a boom. However，what have been done on ecological environment governance，restore and protection of the Qilian Mountain is far from enough，the concept of green development should be firmly set up in the new period of ecological civilization construction，the traditional GDP evaluation mode should be changed，the new mode of environmental improvement and governance should be advocated，“ecological-and-sustainable-lifestyle residents” should be actively cultivated，the mechanism of “community co-management” and “collaborative governance” should be set up，the indigenous citizens should be encouraged to participate in the Qilianshan Mountain reserve management so as to realize the long-term effect of the new mechanism of the Qilian Mountain ecological protection and green development.