Variations in the suspended sediment on the Qinghai–Tibet Plateau have important implications for aquatic ecosystems. Although changes in the cryosphere induced by climate change have been shown to increase sediment yields, their impacts on water and sediment dynamics in headwater regions remain poorly investigated. Here, we examined the responses of runoff and suspended sediment dynamics to changes in the climate and ground freeze–thaw cycle in the source region of the Yangtze River (SRYR) from 1964 to 2019. Long–term daily in situ water and sediment observations provided evidence that climate change controlled change in seasonal and annual water–sediment dynamics by regulating air temperature and precipitation. Attribution analysis showed that precipitation (∼41.93 %, through driving rainfall splash, overland flow erosion, and mass wasting) and land surface temperature (∼30.66 %, through driving freeze–thaw erosion) were the major factors contributing to increasing fluvial sediment fluxes over the past 30 years. We found that freeze–thaw cycles changed the soil erosion patterns by governing the thermal state of the near–surface active layer and driving associated thermal processes. Furthermore, the extension of the thawing duration and the advance of the thawing starting date (at an average rate of 13.5 days/10 yr) exacerbated freeze–thaw erosion, leading to elevated sediment fluxes in the initial thaw and initial freezing periods. This study highlights the need to focus on cryosphere–hydrology observations in terms of sediment dynamics; these findings are critical for soil and ecological protection in alpine headwater regions.