The relationship between system efficiency and pump efficiency in low-head pumping stations depends on the hydraulic losses of its suction box and discharge passage. Based on the summary of the existing main methodologies for the relationship, the conventional basic hypothesis was verified and the antithesis discovered. The system efficiency was equal to the product of the passage efficiency and the pump efficiency; the passage losses occurred when there was no pump. Using CFD technology, the passage losses at different specific speeds modeled impellers with different types of suction boxes. Discharge passages were calculated and the relationship between the loss and flow rate in different systems was analyzed. When the passage loss was one with the pump, the product of the passage efficiency and the pump efficiency expressed the system efficiency. Near the optimal efficiency of the pump, the system efficiency expressed by the passage efficiency without the pump was nearly equal to the test results. The whole system, including the pump, must be considered for the optimal hydraulic design of the system.