The conventional carrier-based cascading PWM method cannot balance the flying capacitor voltage for flying capacitor multilevel inverter (FCMLI). This paper improves the conventional phase disposition PWM method (PDPWM) to achieve the balance of the flying capacitor through adding the link selection of zero level which will be a reasonable allocation of zero level vectors. The carrier waveform will change with different modulations. Its line voltage harmonic performance is greatly improved than that of the conventional phase-shifted carrier PWM method (PSPWM), especially under middle modulation index region. The validity of the novel PWM method is demonstrated by the simulation results.