Qilian Mountain is an important ecological barrier in northwest China，the maintenance of the ecological environment in Qilian Mountain National Nature Reserve is an important premise of the ecological safety in northwest China. Qilian Mountain National Nature Reserve has experienced a serious damage in the past 60 years，the defects existed in the related system and the mechanism is one of the main reasons for its perennial damage. This article will put forward to the following suggestions in terms of the implementation of environmental improvement and governance which is the only way to effectively promote the management system innovation in Qilian Mountain National Nature Reserve based on the author's many-year working ＆ study experience，the analysis of current management system ＆ mechanism and existing problems：①Setting up a comprehensive law enforcement supervision bureau in Qilian Mountain National Nature Reserve；②establishing community co-management mechanism；③Constructing ecological poverty alleviation mode and establishing sound ecological compensation；④cultivating “Ecological-and-sustainable-lifestyle Residents”，changing the idea on ecological emigration；⑤establishing environmental information disclosure mechanism；⑥implementing independent monitoring and evaluation；⑦carrying out distinctive ecological education；⑧implementing green finance；⑨taking ecological assessment instead of “GDP” appraisal mode；⑩the government taking responsibility of buying social services，giving the third party a chance to play to certain role；encouraging the public participation. Try to make our contribution to our national ecological civilization construction for the next one thousand years，provide helps for career development experience in other natural resources protection areas in China through the implementation of environmental improvement and governance，improve the present “paralysis” status of management system and mechanism in Qilian Mountain National Nature Reserve.