In order to study the relationship between the flow and sediment concentration of the gravity settling basin and the water-sediment separation efficiency, this paper sets up a CCHE2D mathematical model for water sediment two phase flows with the aid of CCHE software and uses the mixed length turbulence model to numerically simulate the gravity settling basin so as to get the flow state of the settling basin, the transport law of suspended load and the water-sediment separation efficiency of the settling basin. In addition, based on the previous studies, this paper further analyzed the influence of flow and sediment concentration on water-sediment separation efficiency of the settling basin when flow and sediment concentration are different. The results showed that when the water flow is from 0.05 to 0.3 m3/s, as the flow increases, the flow rate quickens, and the sediment carrying capacity increases, which is not conducive to sediment deposition and will reduce the water-sediment separation efficiency of the settling basin and change the initial sediment content (5 to 20 kg/m3). As the initial sediment content increases, some sediments will be directly brought into the clean water basin because of the existence of tail reflux area of the sediment basin, which will reduce water-sediment separation efficiency of the settling basin.