The three-level neutral-point clamped voltage source inverter (3L-NPC-VSI) is widely used in the maglev traction systems due to its high output voltage, large output capacity and low output current harmonics. In order to improve the utilization of the DC-bus voltage, an overmodulation strategy is necessary. This paper proposes an improved overmodulation strategy based on the minimum amplitude error method for a 3L-NPC-VSI. Compared with the conventional overmodulation strategy based on the minimum amplitude error method, the utilization of the DC-bus voltage is higher. Meanwhile, a virtual space vector modulation strategy is adopted for inverter neutral-point (NP) voltage balance and common-mode voltage (CMV) suppression. Furthermore, the suppression of leakage current also has been verified. Furthermore, the implementation details of the proposed overmodulation strategy based on minimum amplitude error method is elaborated. The effectiveness of the proposed method is verified by simulation and experimental results.