The medium-voltage multi-phase open-winding motor and the multi-phase three-level neutral-point clamped (3L-NPC) H-bridge inverter are the preferred solutions for large-tonnage ship propulsion systems. However, the multi-phase 3L-NPC H-bridge inverter is different from the traditional three-phase inverter, and its output has no common end. In this paper, the neutral-point voltage control of space vector pulse width modulation (SVPWM) is studied. First, according to the principle of minimum common mode voltage, the switching vector is selected, and the five-stage SVPWM method is adopted. Second, the shortcomings of the traditional neutral-point voltage balance method affected by the load power factor are analyzed, since this limits the low-speed operation of ship propulsion. On the basis of the above, an optimization method of neutral-point voltage control based on SVPWM is proposed, which can realize the neutral-point voltage balance control in the full power-factor range. Finally, a twelve-phase 3L-NPC H-bridge propulsion system test platform is used to verify the feasibility and correctness of the proposed optimization method. Results show that the proposed optimization method is feasible and correct. The research in this paper provides a viable method for the neutral-point voltage balance control of a 3L-NPC H-bridge ship propulsion system under low power-factor operation.