We took Poyang Basin as a study area to explore runoff variances during the past 1000 years and the response to climate changes. First, we generated meteorological data for the past 1000 years using climate models CCSM4 and ECHAM5. Then the hydrological model of Poyang Basin was driven using the downscaled meteorological data to produce runoff series. We analysed the characteristics of extreme dry and wet events, the periodic change and the frequency of droughts and floods with fast Fourier transformation and wavelet analysis. It is concluded that both climate models are capable to reflect climate changes during Middle Warm Period and Little Ice Age, indicating a longer dry period in Little Ice Age. There is a good relationship between simulated runoff and precipitation, showing that the drought and flood events have a similar frequency with the minimum and maximum values in precipitation. Also, they have the similar primary period of about 30 years and sub-cycle of around 10 to 15 years and 7 years. The significant signal of 30 years in wavelet power spectrum contours illustrates that such period is consistent with Pacific Decadal Oscillation, which is the main circulation mechanism of the North Pacific climate. Hence, atmospheric circulation oscillation may be the main reason causing meteorological and hydrological changes. This paper extends the current studies on hydrological variances based on data records for the recent 60 years, to a time scale of thousand years. Under the background of global warming, this study helps better understand the mechanism and change patterns of drought and flood events in the middle reaches of Yangtze River.