Estimated daily flows along the Yarlung Zangbo River (YZR) for periods well before stream gauging began in the 1950s are needed to characterize long-term flow variabilities. To examine whether the recorded flow in recent decades can sufficiently represent natural variability and change, daily flows were reconstructed using the autocalibrated variable infiltration capacity (VIC) model using preinstrumental proxy-based precipitation and temperature data for four mainstream stations in the YZR basin for the period 1473–2000. VIC performed well during calibration and validation for all stations, with the Nash-Sutcliffe coefficient of efficiency exceeding 0.55 and the correlation coefficient and the bias in the standard deviation being close to 1. This study showed that the annual or decadal flows have not significantly changed over the past 528 years. The long-term mean flow differed from that for the period 1951–2000 by only 6%–8%, although the reconstructed maximum annual flow was approximately 24%–35% higher and the minimum flow was 0%–9% lower than those for 1951–2000. Moreover, the flow in recent decades could not capture the persistently high or low flows and some extreme wet/dry years found in the preinstrumental period. The timing of the maximum daily flow was more concentrated, and its magnitude was slightly but not significantly higher. A comparison of flows at the four mainstream stations indicated that the annual and peak daily flows were not synchronous. The timing of floods was highly correlated among the three stations, apart from that at Lazi. Furthermore, flows at Nuxia demonstrated a pronounced response to the Indian Ocean Dipole approximately at 20-year periodicity, whereas those at Lazi were more strongly influenced by the North Atlantic Oscillation on an ~50-year scale. This study improves our understanding of the long-term flow variability for the whole YZR basin and its potential climatic drivers for better water resource management and more effective flood hazard control.