Pulse width modulation (PWM) methods are important for the detection performance of a sound navigation and ranging (sonar) system because they determine the output noise of the system. However, only few studies have been conducted on PWM methods for reducing harmonics of a sonar system. In this study, we propose a discontinuous pulse width modulation (DPWM) method for three-leg two-phase (3L2P) inverters. Further, we derive a complete harmonic solution for a double-variable-controlled waveform for the proposed DPWM and conventional continuous pulse width modulation (CPWM) methods. Using these harmonic solutions, we analyze the normalized weighted total harmonic distortion (NWTHD) characteristics according to the modulation index (MI) of the inverter and phase difference of the output voltage for each method. Further, based on the results, we present a superiority map between the conventional CPWM and proposed DPWM methods in terms of the NWTHD. An NWTHD measurement experiment was performed to verify the proposed method. The experiment included additional evaluations of switch losses, phase difference variability, and voltage utilization, which are important factors for sonar systems. This is because improving only NWTHD performance while other factors degrade is not very useful. The results of the experiment confirm that the NWTHD for the proposed DPWM method was 92.5% of that for the conventional CPWM method. We confirm that the mean error of the NWTHD between the analytical and experimental values under similar conditions was less than ~2.2%. In addition, it was verified that the important factors, except NWTHD, were the same throughout additional experiments. Therefore, if the CPWM or DPWM method is selected based on the proposed selection criteria, realizing advantageous operation in terms of the NWTHD is possible.