Understanding the effects of climate variability and reservoir operation on runoff is important for shipping, irrigation and water supply services, especially during extreme drought years. After the operation of the Three Gorges Dam (TGD) began, the discharge processes in the mid-lower reaches of the Yangtze River were completely different from those during the pre-dam period. The measured hydrological data and the Mike 11-HD model were used to estimate the contributions of the TGD operation and climate variability to the variation in discharge during extreme drought years. The results are as follows: under the effects of the TGD operation and extreme drought, the special phenomenon of a "positive discharge anomaly in drought season and negative discharge anomaly in flood season" occurred compared with the conditions in the pre-dam period. During the flood season, the contributions of climate variation (TGD operation) to the changes in streamflow from Yichang station to Datong station were 86.6% (13.4%) and 80.7% (19.7%) in 2006 and 64.8% (35.2%) and 71.3% (28.7%) in 2011. During the dry season, the values were 81.2% (18.8%) and 93.9% (6.1%) in 2006 and 59.9% (40.1%) and 72.9% (27.1%) in 2011. Clearly, climate variation was the main reason for the variation in seasonal runoff. Furthermore, even in the 156 m and 175 m impoundments, climate variation was the dominant factor.