With the increase of operation cycle in long-distance water conveyance project, the problem of silt or algae residue deposition in river channels is becoming more and more prominent, especially in the vicinity of some uncommonly used bifurcation and outflow gates along the water conveyance project. When the deposition reaches certain thickness, it will not only affect the water quality of local water bodies, but also seriously affect the normal operation of these bifurcation and outflow gates. In order to alleviate this problem, the prevention and control of algae residue deposition in long-distance water conveyance project is mainly explored from two perspectives: (1) the scouring effect on the bottom of the side channel is compared by studying different diversion ratios of the side channel; (2) The arc guide wing wall is built near the junction of the main channel and side channel. The simulation is conducted at 6 different included angles including −10°, −5°, 0°, 5°, 10° and 15°, and for non-guide wing wall. The incoming flow is simulated at 280 m3/s of general flow and 320 m3/s of design flow. A total of 14 groups of experiments are carried out for numerical simulation. It can be concluded that, when the incoming flow is held constant, a higher diversion ratio results in a more effective scouring of the bottom sediment in the side channel; when the included angles of the guide wing wall are −10°, −5°, 0° and 5°, it has a significant effect on the prevention and control of algae deposition near the junction; when the included angles of the guide wing wall are 10° and 15°, it cannot play a role in prevention and control and also hinders the normal operation of the river channel.