The rainfall in the south region of Xinjiang is rare which caused severe problems of soil salinization. The salt leaching of farmland and wastewater draining from irrigating farmland are rich in sodium which indirectly leads to the ecological pollution. To effectively deal with the excessive salinity of agricultural wastewater from alkali draining ditches, a shunting device was invented. Firstly, the feasibility of the theory to design the preliminary device was introduced. Secondly, improvement of the device in its functionality and efficiency was given. Finally, numerical simulation of the streaming process of agricultural wastewater based on the computational fluid dynamics utilizing the software fluent was obtained. The derived results were used for the ultimate design of the shunting device. The test conditions were categorized into three groups. The inlet flow rate was set as the only variable, and the spatial distribution of inlet salinity among three groups was assumed to be identical. Two Y axis sectional velocity field cloud diagrams and four X axis sectional salinity field cloud diagrams were selected for detailed comparison. It showed that the shunting device can separate water based on salinity distribution, and agricultural wastewater with low salinity was obtained from the lower diversion trench, vice versa. The efficiency of the shunting device depended on its size, stratification flow velocity and salinity distribution. Adjustment and optimization should be subjected to the actual situation.