Neutral point voltage unbalancing is one of the key issues faced by Vienna rectifier, which causes line current distortion, higher device stress, and eventual failure. This unbalancing is caused by the neutral point current which is a function of modulation strategy. The distribution of the dwell time of a space-vector between its redundant switching states impacts this neutral point current. But the model between the neutral point voltage and the distribution factor is non-linear. Therefore, the existing control strategy based on the small-signal linearized plant is not effective to mitigate the unbalance. This paper proposes an alternative control strategy where the plant becomes linear under large-signal variation. Hence, a simple controller can balance the neutral point voltage on a cycle-by-cycle basis. It also nullifies the DC offset across the capacitors during start or transient. A carrier comparison based implementation of the proposed control is also proposed. The proposed strategy is verified through simulation and experiment on a 1 kW hardware prototype.