Fuel cells are being increasingly used in shipboard microgrid applications because of their low carbon, low noise, and high efficiency. However, the system stability, energy storage durability, and fuel economy of fuel cells should be improved. Therefore, a novel hierarchical energy management method was proposed for achieving virtual impedance droop control according to the ship's operating conditions and lithium battery state of charge (SOC). Unlike the decentralized energy management method, the proposed method can simultaneously achieve lithium battery SOC recovery and improve fuel economy. These results were verified through simulations.