Green airborne transportation driven by the state-of-the-art turboelectric propulsion technology has received considerable attention from the aviation industry. To generate electrified thrust, three-level neutral-pointclamped (3L-NPC) converter-fed motor drives are the most promising candidate for the powertrain of future aircraft. However, the neutral-point (NP) potential fluctuation and deviation lead to harmonics and imperil the lifespan of semiconductors and capacitors. Besides, excessive power losses on the converter limiting propulsive power shorten the flight distance. To solve these issues, a new hybrid modulation strategy is proposed in this paper. With respect to the takeoff and climbing featuring NP voltage drift-prone regions, carrier-based (CB) coordinate-driven modulation waves enabling virtual-space-vector (VSV) are exploited. As for those operating points with high power factor at the cruise, by reconstructing modulation waves, not only can the NP voltage balance be realized, but also the switching loss is reduced by active discontinuous pulse trains. The less computational burden is attributed to implementations in the sextant-coordinate system. The effectiveness of the proposed algorithm is verified by simulation results from a Simulink/PLECS model and experimental results obtained from a 200 kVA silicon-carbide (SiC) based T-type 3L-NPC prototype with a variable output fundamental frequency.