The invention discloses a low common mode vector modulation method and system for a three-level SNPC inverter, and the method comprises the steps that a three-phase current is ssmpled, a reference voltage vector is obtained under an alpha-beta coordinate system, and a sector where the reference voltage vector is located is judged according to the value of a phase angle; a small vector is selected according to the sector where the reference voltage vector is located and the midpoint potential condition, and the action time of the small vector is adjusted through a PI controller; the action time of the large vector, the virtual medium vector and the zero vector is calculated; meanwhile, switch sequences of a coupling part and an independent part of the three-level SNPC inverter is separately designed, wherein the large vector, the small vector and the zero vector are low common mode vectors; and on-off of a power switch tube in the three-level SNPC inverter is controlled based on the action time and the switch sequence so as to control operation of the three-level inverter. According to the invention, the common-mode voltage is effectively suppressed, and the balance of the neutral-point potential is realized.