After the Morakot storm occurred in 2008, the government of Taiwan began the massive sediment dredging in the upstream river, so as to prevent the sediment disaster. However, the volume, location and depth of sediment dredging should be estimated reasonably, so as to provide the dredging basis of engineers. Firstly, this study adopted the estimation method of sediment dredging proposed by previous study to calculate the possible sediment deposit volume under the rainfall depth of 50 years return period. Secondly, the ground elevation after deposition was achieved by elevation overlaying in ArcGIS software platform. Finally, the cross sections of cut & fill depth were designed. This study also used the Ma-Lun creek, Yilan county, Taiwan as the example, to illustrate the plan and design procedure of sediment dredging.