To clarify the influence of key shape parameters on the characteristics of water and sediment in the channel and sediment transport pipe, numerical simulations of the water and sediment two-phase flow in the desilting channel with swirling flow were conducted based on the model experimental test. The results show that the height of the swirling flow generator significantly affects the sediment trapping efficiency, with a maximum difference of 5.41%. The diameter and inclination angle of the sediment transport pipe, and the outlet width of the swirling flow generator have significant influences on the split ratio, with a maximum difference of 8.13%. Increasing the inclination angle improves the sediment accumulation caused by wall conditions at the closed end of the sediment transport pipe. The outlet width of the swirling flow generator has no evident effect on the characteristics of water and sediment in the channel. The desilting channel with swirling flow can discharge sediment efficiently and continuously in all types of desilting channels, with sediment trapping efficiency greater than 90%. After passing through the swirling flow generator, the water with high sediment content flows out of the sediment transport pipe, and the sediment content in the downstream channel decreases sharply.