Restoring natural runoff is an important basic work for water resources allocation under the existing conditions of the underlying surface. In this paper, SWAT as a distributed hydrological model was used to calculate natural runoff quantity. We applied the methodology to the Dawenhe River Basin, and selected three typical sub-basins named the Xueye Reservoir, Huangqian Reservoir and Dongzhou Reservoir, which can generally reflect the natural runoff situation of the basin because of less impact by hu man activities. Then we calibrated and validated the model parameters and analyzed uncertainty of the model by using the SUFI-2 method. After that, we distributed all the sub-basin parameters into the whole basin based on the proximity and similarity principle and analyzed surface water resources of Tai’an City in the Dawenhe River Basin with ArcSWAT2012. The results show that P -factor in three typical sub -basins is larger than 0.64, and R -factor is less than 0.72. The relative correlationand Nash efficiency coefficient is larger than 0.77 during the periodic and validation periods. The higher fitting degree between the runoff simulation value and the measured data demonstrate that restoring natural runoff by SWAT model is feasible.