Climate and land use changes are very important factors that directly influence water resources. To predict runoff under climate and land use changes in Ningxia Qingshui River Basin, which is a typical basin located in the arid and semi-arid area of Yellow River Valley, the distributed hydrologic SWAT model was calibrated and validated using the coefficient of determination (R²) and Nash-Sutcliffe coefficient (Ens) at the Hanfuwan and Quanyanshan hydrological stations. Several future climate and land use change scenarios for the year 2020 were set using the climate historical trend and CA-Markov model. The calibration and validation results for Hanfuwan station showed that R² was 0.80 and 0.71, and ENS was 0.77 and 0.69, respectively, while the results for Quanyanshan station showed that R² was 0.66 and 0.63, and ENS was 0.62 and 0.56, respectively. The results suggested that the SWAT model could be used to predict the runoff under climate and land use changes in Qingshui River basin. Further, our results showed that runoff was dominated by precipitation, and the result under the scenario of reduced precipitation combined with increased temperature had the largest impacts. Runoff can be expected increase in the future land use scenarios because of the increasing farmland and built-up area. Under natural growth, planned development, and woodland/ecological protection scenario, the runoff in 2020 would increase by 17.04%, 14.44%, and 13.98% respectively compared with 2010. Lastly, the runoff change in 2020 was predicted by SWAT model under the combine of land use scenarios and climate change scenarios. The results showed that the runoff would decrease in the future under all combinations of scenarios. Among them, the runoff decreased perceptibly under the combination of planned development scenario and climate changes, and the woodland/ecological protection measure is helpful to slow down the rate of runoff decline under all climate change scenarios in the future. Therefore, in the context of climate change, ecologically prudent constructions and land-use managements are necessary to cope with the severe situation of runoff change in Qingshui River basin.