The establishment and operation of one hydropower complex will change the movement law of water flow and sediment of the river way, and sediment deposition is difficult to avoid. Due to the characteristics of “large amount of sediment, small storage capacity of reservoir”, the desilting operation mode and structure layout design is one of the major technical issues for proposed Karot Hydropower Project. This paper applies a combing method of one-dimensional hydrodynamic & sediment model and a physical model test of dam area to study the movement law of flow and sediment in reservoir and damsite area, then find the rational flushing operation mode and desilting structure layout. The 1-D mathematical model results show that the appropriate reservoir operation mode is “desilting operation water level of 446 m, desilting startup flow of 2100 m³/s”, which can be ensured that the 20-year-operation reservoir will basically reach the scouring and silting balance and the reservoir will be able to regulate the capacity, according to comparison and analysis of sedimentation amount and pattern of various proposals. The 1:100 sediment overall model test results show that the desilting facilities and the desilting dispatching method can ensure the “clean inlet” at the water inlet of power station and also the normal water diversion and power generation, and for which are consisted of 6 flood discharge surface orifices and 2 flood discharge and desilting orifices. The results of this study can be used for providing scientific bases for Pakistan Karot Hydropower Project design.