In the arid areas of northwest China, the high sediment concentration of the Yellow River poses a great threat to the safe and efficient operation of pumping stations. In order to explore the influence of sediment deposition on the hydraulic characteristics of the inflow system of the pump station, this study uses the reverse engineering technology to reconstruct a typical inflow system, and obtain the real computational domain model of the structure in the siltation state. By combining the Realizable k-ε model and the Mixture model, “Fluent” is applied to carry out numerical calculations and analysis of water-sediment two-phase flow within the inflow system. The numerical calculation results are compared with the measured values to verify the reliability of the simulation. The results indicate that the reverse modeling method can accurately reflect the complex sedimentation characteristics and boundary conditions. The sedimentation generated by long-term operation gradually narrows the water passage along the water depth, increasing the head loss of the flow field by 56.32% compared to the flow field without sedimentation; the maximum volume fraction of the near-bottom sediment increased by approximately 39% compared to the preliminary stage; the uniformity of flow velocity distribution on the characteristic cross-section of the suction pipe has decreased.