This paper proposes the pulse width modulation (PWM) control strategy for low-speed operation in the three-level neutral-point-clamped (NPC) inverters based on the bootstrap gate drive circuit. As a purpose of the cost reduction, several papers have paid attention to the bootstrap circuit applied to the three-level NPC inverter. However, the bootstrap gate driver IC cannot generate the gate signal to the IGBT for low-speed operation, because the bootstrap capacitor voltage decreases under the threshold level. For low-speed operation, the dipolar and partial-dipolar modulations can be the effective solution. However, these modulations have drawbacks in terms of the switching loss and THD. Therefore, this paper proposes the PWM control strategy to operate the inverter at low-speed and to minimize the switching loss and harmonics. The experimental results are presented to verify the validity on the proposed method.