The traditional discontinuous pulse width modulation (DPWM) strategy is very suitable for reducing the switching losses of three-level inverter (TLI). However, large neutral point voltage (NPV) fluctuation is usually caused, which results in low frequency harmonics (LFHs) in the output line voltage. Therefore, a DPWM modulation strategy that can suppress LFHs is presented in this paper, and it is recorded as low frequency harmonic reduction DPWM (LFHRDPWM). The proposed LFHRDPWM can be seen as an improvement of traditional DPWM, which modifies the duty ratios according to voltages of the two DC-link capacitors. For LFHRDPWM, due to the suppressed LFHs, the self-balancing ability of NPV is thus lost, and gradually increased DC offset on NPV is caused. To overcome that, an active neutral point voltage control (ANPVC) method is also proposed. The proposed methods not only can achieve switching loss (SL) reduction almost as the same as traditional DPWM strategy, but also can realize NPV control and LFHs reduction. The effectiveness of the proposed method is verified by experiments.