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Due to the limitation of voltage capability and current capability of power devices, it is very difficult to handle nonlinear loads for traditional active power filters(APF) with two-level inverter in high voltage high power grid. Three-level NPC inverter has been put into practical use for years especially in high voltage high power grid. The application of such converter to APFs is hindered by the problem of voltage unbalance of DC capacitors that leads to system instability. This paper presents a close-loop digital control algorithm of DC voltage for this APF. The PI controller regulates DC voltage in the outer-loop controller. In the current-loop controller, this paper researches the issues of neutral-point voltage control from the space vector PWM (SVPWM) point of view in detail. Then this paper proposes a simple neutral-point voltage control method. The experiment results illustrate that the performance of the proposed approach is satisfactory.