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Reservoirs play an important role in responding to natural disasters (such as flood and drought) by controlling the runoff. With the climate changing, the frequency and intensity of flood and drought are likely to increase. Thus, the impact of reservoirs on runoff under climate change needs to be studied to cope with future floods and drought. In this study, the Nierji Reservoir located on the Nenjiang River Basin was chosen to explore the impact. The Nenjiany River Basin is the vital water source in the water resources transfer project in Northeast China. Climate change in Nenjiang River Basin was analyzed using the 1980 to 2013 climate observations. The results show that the temperature of the basin significantly (p < 0.05) increased while the precipitation significantly (p < 0.05) decreased. Based on the result, nine kinds of different climate scenarios were set up. For different climate scenarios, the Hydroinformatic Modeling System (HIMS) model and the HIMS model with the reservoir calculation module were used to simulate runoff during the no reservoir operation period (1980-2000) and reservoir operation period (2007-2013), respectively. The impact of reservoirs on runoff under climate change is studied. Results show that the Nierji Reservoir can effectively relieve the impact of climate change on downstream runoff. When temperature increases or precipitation decreases, there are larger differences in runoff over the non-flood period, especially during periods of no reservoir operation. Reservoir operation under climate change can provide reliability in drought protection.