Abstract: The uniform flow patterns of the pump intake system can dominate the efficient and stable operation of pumps. The for-bay, pump sump, and intake pipe are composed of the pump intake system in a pumping station. A large number of pumping stations in China are generally operated under the condition of sediment, particularly in the Yellow River Basin. The deposition of sediment in the pump intake system can deteriorate the flow uniformity during operation. The distribution of sediment concentration mainly affects the uniform pump intake flow, when the pumping station operates with the sediment inflow under the design water level. In this study, the Euler two-phase simulation was conducted to investigate the influences of the combination of start-up pumps on the sediment concentration distribution in the intake flow field of a large-scale pumping station. One kind of sediment particle size and one kind of sediment concentration were employed in the numerical simulations for a large-scale pumping station in Ningxia Hui Autonomous Region, China. Firstly, a comparative analysis of the single-phase and two-phase model was carried out to quantify the influences of sediment on the uniform intake velocity and the recirculation coefficient of the intake flow field. The presence of sediment affected the velocity distribution and vortex characteristics of the intake flow field in the pumping station. It was found that the recirculation coefficient of the pump intake system increased by 20.6%, whereas, the uniformity of the intake velocity decreased by 8% when the particle diameter was 25 μm and the sediment concentration was 10 kg/m3. Secondly, an investigation was made to clarify the influences of the number and position of start-up pump units on the sediment concentration. Another comparative analysis was performed on the design operating case with six pumps, two cases with five pumps, three cases with four pumps, and two cases with one pump. There was a high sediment concentration on the two sides of the fore-bay and pump sump and a low one in the central region. The sediment concentration on the two sides of the intake flow field increased, as the number of the start-up pump unit decreased. There were the severe negative effects of the unutilized side pump unit on the symmetry of the intake flow field, resulting in the dead water zone or vortices for the higher sediment concentration. A quadratic polynomial model of the start-up pumps and sediment deposition efficiency was established to determine the sediment concentration distribution in the multi-cases with different numbers and positions of start-up pump units. Finally, a correlation analysis was performed on the sediment concentration and transverse velocity. There was a power function correlation between the sediment concentration and the transverse velocity square at the bottom of the fore-bay and pump sump, even at the slice 0.2 m from the bottom of the pump sump. The trends of the sediment concentration and the transverse velocity were consistent in the direction of water depth. In multiple cases with a different number of start-up pump units, there were also the power function correlations between the sediment concentration and transverse velocity square, but the constant coefficients of the correlations were slightly different. The power function models indicated that the critical deposit velocity of the intake flow field was 0.421 m/s in the design operating condition when the particle size was 25 μm and the sediment concentration was 10 kg/m3. The critical deposit velocity decreased significantly, as the number of the start-up pump unit decreased. The achievements have theoretical significance and engineering applications for the high hydraulic performance of pumping stations.