A modified virtual space vector based DC-link voltage balancing strategy is proposed in this paper. The summation of the three phase currents for the virtual vector needs not to be zero and it also keeps the two capacitor voltages balanced over a wider range of load variations. The duty cycles for all the power switches are also derived in this paper. Due to the reduced use of medium voltage vectors the proposed control strategy can considerably decrease the neutral point voltage fluctuation for lower power factor based loads as well. Detailed simulation and experimental studies are also carried out to show the effectiveness of the proposed system with a DC-link voltage balancing strategy. Voltage and current harmonic distortions are also presented with change in modulation index. A Dspace® based real time operating system is used experimental validation with a 6.0 kW surface PMSM.