When the agricultural non-point source runoff is transported to waste water treatment plant by sewage interception trunk around Dianchi Lake, the TP concentration will decrease along the way and be lower than the designed influent concentration at the end of trunk, which results in the failure of meeting the discharge standard. In order to explore the influence of main design parameters on end TP concentration and provide technical reference for the design of sewage interception trunk, the conducted research focused on the granular phosphorus in the agricultural non-point source transported by the well-constructed sewage interception trunk on the east bank of Dianchi Lake. The three-dimensional simulation software FLUENT was used to build the multiphase flow model of the fluid in sewage interception trunk and simulate the flow process. The influences of different section shape, roughness, hydraulic diameter, slope on the end TP concentration were analyzed. The simulation results show that the end TP concentration for the circular cross section is the lowest and is the highest for the trapezoidal section. With the increase of the roughness, the end TP concentration for the three section shapes increases, and there is a small variation range of the end TP concentration for rectangular section, while the largest variation range is for the circular section. With the increase of hydraulic diameter or slope, the end TP concentration for rectangular or trapezoidal section increases or decreases, while that of circular section decreases or has little change.