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[Display omitted] • Finding the extension of ablation period and the accelerative warming in TRHR; • Finding runoff increased and seasonal pattern changed; • Finding multiphase water transformation influences the runoff recharge sources. The present study focuses on the influence of multiphase water transformation on the hydrology of the Three-River Headwater Region. Climatic factors, accelerated transformation of water bodies, and changes in runoff patterns were evaluated based on long-term field observations. Subsequently, we estimated that changes in climatic factors have prolonged the ablation period and accelerated warming since 1990. Additionally, the glacier retreat rate during 2001–2013 was accelerated by approximately 16.23% compared with that during 1976–2001, whereas the ratio of snowfall in annual precipitation has decreased by 2.37% since 1990. The beginning of the freezing cycles of lakes along with the complete cycles were delayed. Moreover, snow sublimation significantly increased after 1990. Amplitudes of frost days (number of days with daily minimum temperature below 0°C) during 1991–2019 were eight times higher than those during 1960–1990. Furthermore, the contribution of moisture recycling to precipitation increased by 9.74% from1979 to 1990 to 1991–2019. The variations in actual evaporation increased from −1.257 mm/a during 1980–1990 to 0.865 mm/a during 1991–2017 and the runoff increased by 66.83×108 m3/10a during 1991–2012. July experienced the highest rainfall and runoff. During the multiphase water transformation, the runoff recharge sources changed significantly, thus, changing the historical trend of recharge in the headwaters of rivers only by the glacier snow meltwater by providing a new recharge mode. However, the accelerated multiphase water transformation caused by climate warming increased the challenges in water resource management and flood control in alpine regions. [ABSTRACT FROM AUTHOR]