Abstract: To investigate the flow characteristics and their impact on operational efficiency of an intake pump station under different start-up combinations, this study takes the inflow and outflow system of the Guanlu Reservoir inlet pump station as an example. Both numerical simulation and physical model testing were utilized. Parameters such as velocity uniformity, inflow angle deviation, hydraulic loss, and pressure pulsation were employed to establish a comprehensive Hydraulic Efficiency Index (HEI) for the quantitative evaluation of hydraulic performance under various operating conditions. The results show good agreement between the numerical simulation and experimental data in terms of flow patterns, hydraulic losses, and pulsation characteristics. Under symmetrical dual-pump operation, the inlet flow pattern is uniform and stable, with a velocity of approximately 0.065 m/s, low energy loss and small pulsation amplitude. The velocity uniformity in the inlet sump reaches 91.5%, and the inflow angle is about 89°. In single-pump operation, the high-velocity zone is concentrated in front of the operating pump (around 0.05 m/s), whereas the overall flow velocity in the forebay remains low (0–0.082 m/s), which is prone to forming stagnant water zones. During asymmetric three-pump operation, the velocity distribution becomes disordered (approximately 0.050 m/s) with evident flow skewness, intensified local recirculation, and increased hydraulic loss. In addition, variations in flow rate significantly affect the flow patterns, hydraulic losses, and pressure pulsations in the inflow-outflow system. The operational range diagram based on the HEI indicates that the optimal start-up unit is the symmetric dual-pump operation, while the single-pump and asymmetric three-pump operations are recommended only for short-term peak-shaving conditions. The research results provide a quantitative basis for the optimal operation and scheduling of similar pump stations.