In the context of global warming, increasing frequency of climate extremes poses a great challenge to natural systems and humankind. However, the spatial and temporal characteristics, as well as the mechanisms of extreme climate change, remain insufficiently understood, particularly in arid and semi-arid mountainous regions with high climate sensitivity and ecological fragility. In this study, we analyzed the spatial and temporal characteristics of 27 extreme climate indices (including intensity, duration, and frequency) in the Qilian Mountains, northeastern Tibetan Plateau, from 1961 to 2016 using the CN05.1 meteorological grid dataset, explored the relationship between the extreme climate indices and internal variability of the climate system (e.g., the North Atlantic Multi-decadal Oscillation (AMO), the Pacific Decadal Oscillation (PDO), and the Arctic Oscillation (AO)), and further probed into the mechanisms affecting climate extremes using ERA5 reanalysis dataset. The results showed that extreme temperatures in the Qilian Mountains were significantly enhanced in terms of intensity, frequency, and duration during 1961–2016. The decrease rates of frost days (FD0) and ice days (ID0) were − 4.4 d per decade and − 4.7 d per decade, respectively, and the increase rate of growing season length (GSL) was 2.9 d per decade. Extreme precipitation intensity increased significantly, with the intensity indices R95P and PRCPTOT showing the most significant change trends of 4 mm per decade and 14.9 mm per decade, respectively (p < 0.05). The number of consecutive dry days (CDD) displayed a significant downward trend, with a rate of −6 d per decade, the number of moderate precipitation days (R10) showed an increasing trend of 0.12 d per decade. Correlation analyses revealed significant associations between the increases in extreme climates and the AMO and PDO. Additionally, the enhancement of the AO contributed to the increased extreme precipitation. Enhanced anticyclonic circulation in Eurasia and geopotential height, as well as increased cloud cover in winter, were the main reasons for the increase in extreme temperatures in the Qilian Mountains, whereas the significant increase in water vapor transport entering the east boundary of the Qilian Mountains in summer mainly contributed to the increase in extreme precipitation. This study highlights internal oscillations in the climate system that regulate the extreme climate variability in the Qilian Mountains at various spatial-temporal scales.