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Shunt Active Power Filters (SAPF) have been proved to be an effective approach to eliminate harmonic current in power grids. The DC voltage control during dynamic processes is critical for the safe and performance of the SAPF. In this paper, soft startup and impact suppression techniques are proposed to guarantee no voltage overshoots or sags in DC bus during startup and other dynamic processes. Subsequently, a novel controller for DC bus voltage regulation is put forward according to the small signal model based on the instantaneous power balance in AC and DC sides of three-phase SAPF. With good compensation effects, the proposed voltage loop controller has improved dynamic performances greatly compared with traditional PI controllers as loads change. Finally, simulation and experimental results from a 260 kVA prototype verify the feasibility of the proposed techniques and control strategies.