Quantification of runoff change is vital for water resources management, especially in arid or semiarid areas. This study used the Soil and Water Assessment Tool (SWAT) distributed hydrological model to simulate runoff in the upper reaches of the Hailar Basin (NE China) and to analyze quantitatively the impacts of climate change and land-use change on runoff by setting different scenarios. Two periods, i.e., the reference period (before 1988) and the interference period (after 1988), were identified based on long-term runoff datasets. In comparison with the reference period, the contribution rates of both climate change and land-use change to runoff change in the Hailar Basin during the interference period were 83.58% and 16.42%, respectively. The simulation analysis of climate change scenarios with differential precipitation and temperature changes suggested that runoff changes are correlated positively with precipitation change and that the impact of precipitation change on runoff is stronger than that of temperature. Under different economic development scenarios adopted, land use was predicted to have a considerable impact on runoff. The expansion of forests within the basin might induce decreased runoff owing to enhanced evapotranspiration.