A two-dimensional flow and sediment model was used to study the sedimentation problem of a high head and high sand content hydroelectric power station in Nepal. Under the layout scheme of “reservoir replacing pool + bypass flushing”, a total of 12 sediment discharge operation schemes were proposed for the reservoir area under the combination of 3 flow limits and 4 sand discharge water levels. The results show that: After 5 years of operation of the project, there is a difference in the elevation of the sedimentation surface in front of the water intake. Different sand flushing operation methods have a significant impact on the elevation of the sedimentation surface in front of the water intake during the period of 7–17 years. Under various schemes, the trend of the elevation change of the sedimentation surface in front of the water intake after 17 years of operation of the head hub is basically consistent, and the difference is not significant. The elevation of the sedimentation surface in front of the water intake can be controlled at around 2505 m under each scheme; When operating at a sand discharge water level of 2520 m, the elevation of the sedimentation surface in front of the sand discharge tunnel can be controlled at around 2510 m, and the probability of sedimentation in the bypass sand discharge tunnel is not high; The project operates for about 10–15 years and is basically in a balanced state; Under the condition of 2520 m sediment discharge water level, the remaining effective storage capacity of the hub is larger after 20 years of operation under each scheme; This project follows the 2520 m sediment discharge water level scheme. When operating at a sediment discharge flow limit of 120 m3/s, the effective storage capacity of the reservoir meets the requirements of the designed daily regulating storage capacity. Therefore, it is recommended that this project operate according to the 2520 m sediment discharge water level scheme.