Climate warming increases the variability in runoff of semiarid mountains where seasonally-frozen ground is widely distributed. However, what is not well understood are the processes of runoff, hydrological drivers, and freeze-thaw cycles in seasonally-frozen ground in semiarid mountains. To understand how freeze-thaw cycles affect runoff processes in seasonally-frozen ground, we monitored hydrological processes in a typical headwater catchment with seasonally-frozen ground in Qilian Mountain, China, from 2002 to 2017. We analyzed the responses of runoff to temperature, precipitation, and seasonally-frozen ground to quantify process characteristics and driving factors. The results show that annual runoff was 88.5 mm accounting for 25.6% of rainfall, mainly concentrated in May to October, with baseflow of 36.44 mm. Peak runoff occurred in June, August, and September, i.e., accounting for spring and summer floods. Runoff during the spring flood was produced by a mix of rainfall, melting snow, and melting seasonally-frozen ground, and had a significant correlation with air temperature. Runoff was mainly due to precipitation accumulation during the summer flood. Air temperature, average soil temperature at 0-50 cm depth, and frozen soil depth variable explained 59.60% of the variation of runoff in the thawing period, while precipitation variable explained 21.9%. Thawing-period runoff and soil temperature had a >0.6 correlation coefficient (P <0.05). In the rainfall-period, runoff was also affected by temperature, soil moisture, and precipitation, which explained 33.6%, 34.1% and 18.1%, respectively. Our results show that increasing temperature and precipitation will have an irreversible impact on the hydrological regime in mountainous basins where seasonally-frozen ground is widely distributed.