The high-speed flywheel energy storage system (FESS) has been used in urban rail transit system to provide network stability and regenerative braking energy recovery due to its merits of high-power density, almost infinite charging–discharging cycles, nonexistent capacity deterioration, and environmental friendliness. The electrical fundamental frequency of the FESS motor/generator will be significantly increased when the rotor is mainly composed of carbon fiber composites to achieve higher speed. In addition, in view of the 1500-VDC power supply of the urban rail transit system, the switching loss of the power switching devices will be significantly increased or the system failure may be occurred when the high switching-to-fundamental frequency ratio (SFFR) control strategy is applied. Therefore, a low SFFR <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$=$ </tex-math></inline-formula> 1 control strategy of the I-type neutral point clamped (NPC) three-level converter for the high-speed FESS with brushless direct current (BLDC) motor in two-phase conduction mode is designed, and the matching midpoint voltage balance strategy is proposed. The effectiveness of the proposed control strategy is verified by simulation and experiments. The stable and low switching loss operation of the high-speed FESS rated at 1500 VDC, 330 kW, and 36 000 r/min is realized, and the midpoint voltage balance is strongly controlled.