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This paper proposes a novel energy management strategy (EMS) of an onboard supercapacitor (SC) for subway applications with a permanent-magnet (PM) traction system. The studied subway train is modeled, and its control is developed, in which the flux-weakening operation is taken into account to minimize the copper loss. The proposed EMS tries to minimize the actual flux-weakening region. Compared with the conventional EMS, the proposed EMS is realized by increasing the dc bus voltage to minimize the demagnetizing d-axis current, hence copper loss, in the flux-weakening region instead of reducing the dc bus voltage drop during startup. An experimental platform using the hardware-in-the-loop (HIL) simulation method is developed, and experiments are carried out to verify the effectiveness of the proposed EMS.