Abstract: Vertical axial-flow pumps have been widely used in the low head pumping station, due to their simple structure, excellent ventilation and heat dissipation, convenient installation, maintenance, and operation. But it is rarely used in the extra-low head pumping station, because the hydraulic performance is less than that of tubular pump. This study aims to improve the hydraulic performance of the vertical axial-flow pump system in the extra low head pumping stations. The numerical simulation was also carried out on the three-dimensional turbulent flow using the Reynolds time mean Naiver-Stokes equation and RNG turbulence model. The flow field of the inlet and outlet channel was calculated in the vertical axial-flow pump system. different submerged depth of the impeller center was selected for each impeller diameter of 3.0, 2.5, 2.0, and 1.5m. Meanwhile, the flow field and hydraulic loss of the flow channel were compared to the hydraulic performance of the vertical axial-flow pump system in the extra low head pumping stations. The submerged depth was set as the pump impeller center of 3.08, 2.38, and 1.68. Finally, the test had validated the simulation. The results show that the submerged depth of the impeller center shared little effect on the flow pattern and hydraulic loss of the elbow inlet channel. The same flow pattern was found in the inlet channel. The hydraulic loss of the channel was basically unchanged under the same impeller diameter and different submerged depths. The flow velocity changed gently and evenly, indicating the orderly turning flow in the elbow inlet channel. There was no bad flow pattern in the elbow inlet channel; There was a large impact of the submerged depth of the impeller center on the elevation arrangement of the vertical axial-flow pump system and the hydraulic performance of the siphon outlet channel. The layout space of the outlet channel increased in the direction of the façade with the increase of submerged depth of the impeller center. The flow pattern was gradually improved in the siphon outlet channel, where the current turned more gently. The hydraulic loss of the siphon outlet channel basically tended to decrease. There was an increase in the efficiency of the pump system. The efficiency was 75.92% at the optimal operating point of the model test under extra low head conditions. The energy performance of the pump system was also consistent with the model test. The increasing submerged depth of the pump impeller center also led to an increase in the investment in the civil engineering of the pumping station. The pumping station can be required to increase the submerged depth of the impeller center, according to the added value of civil investment and the reduced value of operating cost. The finding can provide a sound reference to design the vertical axial-flow pump system in the extra-low head pumping stations.