Landslide, debris flow and flood with high sediment concentration usually induce a great quantity of sediment deposits in the upstream river. If the sediment deposits cannot clean up in time, the people lived beside the river may fall into the danger of debris flow while storm happens. There are a interesting topic is: How much volume of sediment deposits should be clear away, so as to prevent the sediment disaster? This study select the Hanxi watershed, Yilan County as the example, to estimate the depth, range and volume of sediment deposit in stream under a rainfall depth with 50 year regression period. Firstly, the historical rainfall depth is collect to estimate the rainfall volume and the rainfall time distribution. Secondly, the hydrological model HEC-HMS is adopted to process the hydrological routing and to obtain the flood hydrograph. Finally, the FLO-2D model is used to finish the two-dimensional hydraulic routing and sediment deposit volume estimation, which will be a basis of sediment cleanness.