In application of active power filters (APF), DC side voltage fluctuation is very common and the secondary pulsation is particularly prominent in this kind of fluctuation. In the study of threephase threewire APF with asymmetric load, it is found that voltage loop is affected by secondary pulsation in some degree and it will generate unnecessary additional negative sequence reference current and reference current amplification effect. As a result, the fundamental negative sequence current in compensation current produced by APF is greater than fundamental negative sequence current produced by asymmetrical load, which causes the asymmetry of the network side current. After secondary pulsant suppressed by notch filter, the reference current amplification effect can be reduced effectively and the network side current will be symmetrical. The simulation and the experiments have proved the correctness of views proposed by this paper.