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Over the past few decades, natural reserves have been affected by both climate change and human activities, and their land cover has changed dramatically, especially in mountain reserves, which are more sensitive to climate change and human activities. This paper used long-term Landsat and MODIS NDVI remote sensing data to monitor the changes of land cover and vegetation conditions in the Qilian Mountain National Nature Reserve (QMNNR) in China from 1975 to 2015, and analysed the impacts of climate change and human activities in combination with meteorological and socioeconomic data. The results show that the land cover structure of the QMNNR has remained stable over the past 40years, but the total area of natural vegetation has decreased by 49.55km(2), the artificial surface and cropland has expanded by 13.68 and 32.57km(2) in some areas, respectively, and the glacier has retreated by 33.34km(2) as a whole. The warming and humidification trend of the climate is the leading factor for glacial retreat and the improvement of the overall vegetation condition, while population growth and economic benefits lead to the expansion of cropland and artificial surfaces in some areas, thus causing the reduction of 18.80 and 28.30km(2) in shrubland and grassland. This study proves that the system of protected areas plays a key role in maintaining the stability of the ecosystem structure and that reducing the population density around the protected areas and changing the mode of economic development can effectively reduce the intensity of human interference. Under the background of climate warming, the change of the ecosystem function in mountain protected areas is full of uncertainty, so management and protection strategies need to be studied in depth.