Abstract: SUFI-2 and GLUE are two widely used calibration and uncertainty analysis techniques for SWAT model in recent years. To compare the strengths and weaknesses of these two techniques, we choose Daning River watershed as the study area to simulate the runoff in watershed by using ArcSWAT2012 and conduct calibration and uncertainty analysis based on SUFI-2 and GLUE respectively. Furthermore, SUFI-2 and GULE were compared in terms of the uncertainty of SWAT output, the fitting effect, the computational efficiency and the parameter uncertainty. The results indicated that both SUFI-2 and GLUE can be well applied to the calibration and uncertainty analysis of SWAT model of Daning River watershed. However, the calibration and uncertainty analysis based on SUFI-2 could achieve smaller prediction uncertainty band and better fitting effect by less simulation numbers, and the parameter uncertainty analysis based on GLUE performs better than SUFI-2. For runoff simulation by SWAT model, the calibration and uncertainty analysis of simulation output is suggested to be conducted based on SUFI-2, while the parameters uncertainty analysis is suggested to be conducted based on GLUE.