Currently, variable-frequency drives (VFDs) are always applied on the motors in variable flow systems to modulate the pump water flow. Meanwhile, multiple parallel pumps are required if a single pump cannot satisfy the required water flow rate. Therefore, the water flow and head demand in variable-flow systems with parallel pumps may be satisfied by either fewer operating pumps at a higher speed or more operating pumps at a lower speed. Parallel pumps should be sequenced based on the water-to-wire efficiency of a VFD-motor-pump system, which combines the efficiencies of the pump, motor, and VFD at any water flow rate and head. However, the motor efficiency is currently not well modeled under variable frequency. The purpose of this paper is to develop an optimal pump sequencing control with an accurate water-to-wire efficiency model. First, the wire-to-water efficiency of a VFD-motor-pump system is improved by applying a motor equivalent circuit method to calculate the motor efficiency at variable frequency, and then the improved wire-to-water efficiency is applied to develop the optimal operating regions for a secondary chilled-water system with three parallel pumps. The simulation results show that the developed optimal pump sequencing control can reduce the system power input by up to 25% over the maximum flow sequencing control and by up to 3% over the best pump efficiency control.