Different from the land-based power grid, the ship power grid is an isolated network with limited capacity. When working with pulse loads with low average power and high peak power, it will have a more serious continuous impact on the power grid. This paper designs a three-level active power filter with supercapacitor energy storage for the current impact caused by the pulse load in the ship. An ANN based method is proposed to control the active power filter, so as to maintain the stability of supply current and avoid the continuous and large impact on the power grid. Based on the method of double closed-loop PI control, the supercapacitor energy storage unit is controlled to meet the energy demand of pulse load, maintain the stability of DC voltage and ensure the APF can work properly. The simulation results show that the proposed topology and control strategy can solve the problem of current impact in the ship power grid.