The Modulation Mode (MM) of three-phase three-level flying capacitor inverters are focused in this paper. Based on Phase-Disposition SPWM (PD SPWM), a novel classification method for Modulation Sequence (MS) is deduced. Then, 11 sorts and 8 types of modulation sequence are analyzed. As modulation index varies, 6 types of modulation modes are suggested in three-phase three-level flying capacitor inverters. Under different modulation index, the THDs (Total Harmonic Distortion) of inverter output voltage and current in a output period are analyzed, the switching times of 4 power devices in an inverter bridge arm are calculated. The results show that MM-4 has the better comprehensive output quality, i.e. lower THD and smaller switching times while the modulation index is between 1 and 1.155. In addition, an innovative design method about flying capacitor is introduced based on PD SPWM. Finally, the MATLAB simulations are completed, the effectiveness and correctness of design and analysis are verified.