To deal with DC voltage unbalance on two arms and the total DC voltage overshoot during startup, three closed loops control strategy of three-phase four-wire active power filter (APF) is shown. The influence of DC voltage on the APF and the origin of DC voltage ripple is analyzed. Besides the DC voltage control targets are presented. Based on the relationship of DC voltage and energy exchange, a method of DC voltage balance on two arms is proposed. A solution is given about the total DC voltage overshoot during startup. As the difference under heavy load and light load, control strategies are selected respectively. At last, experiment is done to verify the principle above.