The advantages of three-level neutral-point-clamped (NPC) H-bridge inverters, such as simple topological structure, low device voltage stress, high equivalent switching frequency, and highly expansible capacity, have made them the preferred choice for inverters matching with medium voltage high-capacity multi-phase open-end winding vessel propulsion motors. To quantitatively evaluate the propulsion motors’ harmonics, electromagnetic vibration, and noise caused by pulse-width modulation (PWM) and device dead-time, it is necessary to research the mathematical modeling of pulse-width modulated output voltage harmonics in consideration of dead-time. In this paper, the principle of the phase-disposition PWM method of the 3L-NPC H-bridge inverters was firstly introduced. Then, the analytical models of output voltage harmonics with and without considering the effect of dead-time were established based on the double Fourier series approach and the harmonic distribution of the dead-time effect was accurately characterized. On the basis of the above, the experimental platform was established to verify the proposed analytical model. Simulation and experimental results are consistent with the theoretical analysis in low and high-frequency output voltage harmonics, which proves the correctness and the feasibility of the analytical modeling method researched by this paper. This will provide a theoretical basis for subsequent studies, which include the quantitative analysis and the suppression of output harmonics of the H-bridge inverter considering dead-time.