Because of the neutral current, the dc voltage balancing control is important but very difficult for the three-phase four-wire APF based on the three-level neutral-point-clamped topology. And existing literatures can’t accurately analyze the potential drift in the three-phase four-wire system. This paper proposes an accurate mathematical model of the dc-side voltages in this APF with parametric perturbation when working under the unbalanced condition. From this model, it can be got that the basic reason of neutral-point potential drift is the unbalanced distribution of active power caused by parametric perturbation. By injecting zero-sequence dc component, the neutral-point potential balancing control can be realized based on the exchange of active power between dc-side capacitors. Simulation and experiments show the effectiveness and performance of this proposed model.