Irrigation water for agriculture in Ningxia during the summer is primarily sourced from the Yellow River self-flow irrigation region. However, the water conveyance system in this region is significantly influenced by hydrodynamic factors, morphological factors, human factors, and the infrastructure used for social purposes, all of which directly impact the irrigation water utilization coefficient. In order to improve the irrigation water utilization coefficient, reduce suspended sediment deposition in the water conveyance channels, and mitigate negative effects on the water supply system, this study implemented a sediment diversion system at the channel head. This is expected to increase water usage efficiency to a certain degree. Using actual data on hydrodynamic factors from the Shizuishan section of the Yellow River in Ningxia, a two-dimensional numerical simulation was performed, and a two-dimensional hydrodynamic model and sediment model of the Shizuishan section of the Yellow River in Ningxia were developed using MIKE 21. The water conveyance method at the channel head was simulated under two different operating conditions. Results indicated that compared to operating condition 1, operating condition 2 had a beneficial effect on diverting and reducing sediment at the fish mouth of the channel head: the sediment accumulation thickness of one day in operating condition 1 was 0.16 m, 0.003 m, 0.15 m, and 0.21 m under actual flow, scenario 1, scenario 2, and scenario 3, respectively; whereas in operating condition 2, the sediment accumulation thickness of one day was 0.11 m, 0.001 m, 0.09 m, and 0.12 m under the same conditions, respectively. Additionally, as the computation period lengthened, the sediment accumulation thickness of operating condition 2 was significantly smaller than that of operating condition 1. In conclusion, operating condition 2 is superior for the design of the channel head in the Yellow River self-flow irrigation region.