The Tibetan Plateau acts as an Asian water tower and amplifies global warming, which leads to increased runoff and sediment flux in Tibetan rivers in recent years. Consequently, downstream areas face an increased risk of flood disasters. However, there is still a lack of clarity regarding the alterations, impacts, and mechanisms involved in runoff and sediment flux based on the latest data. Here, the cumulative anomaly, sliding T-test, and M-K trend test were employed to analyze the temporal mutation of meteorological and hydrological data (1957-2023 CE) from Yangtze River headwaters. The analysis revealed three distinct periods: P0 (1957-2004), P1 (2005-2016), and P2 (2017-2023), and demonstrated that (1) the maximum monthly runoff shifted from July (P0-P1) to September (P2) due to increased icemelt; (2) the ratio of September sediment flux to annual increased from 13% (P1) to 20% (P2); and (3) the percentage of temperature contribution to runoff increased from 44% (P1) to 57% (P2), overtaking that of the precipitation. In September the warming-driven increase in runoff overlapped with sediment flux increase caused by reduced sediment fixation capacity of vegetation. Our findings, which reveal that global warming drives both runoff peak shifting from July to September and sediment flux sharp increase in September, are critical for future disaster prevention and siltation control in downstream regions.