In order to solve the problem of poor re-producibility and large particles in pulse bias arc ion plating (AIP), this paper proposes an incremental fuzzy control scheme based on the extended state observer(ESO) for DC/DC converter. According to researches about equivalent load model of pulse bias AIP in the vacuum environment, the relationship between the influence factors on load and output performance is discussed. Then, based on the small signal model of DC/DC converter, a new 3-order mode-compensation ESO is built to decrease the observing error. In addition, the method of phase plane for designing fuzzy control rule is presented to optimize the rule, and the stability of designing fuzzy control system is analyzed by the Lyapunov theory. The simulation and experimental results have demonstrated that the tracking performance and robustness of pulse bias power supply with the proposed scheme are significantly improved.