Wireless power transfer (WPT) system is emerging in the marine application as more ships are becoming battery-powered. In this paper, a control method is proposed for a high-power wireless chaging system for charging electric ship. In the marine application, the ship is subject to continuous horizontal and vertical misalignment due to sea waves. Battery charging time is another challenge, especially in time-demanding mission-critical operations. To address these new issues, the sensitivity of a WPT system to the variation of magnetic coupling and load has been analytically investigated, and a new adaptive control method has been proposed. The analytical model has been verified through the simulations that emulate the variation of the mutual inductance in marine applications. The proposed control has been experimentally validated using a 5 kW prototype wireless charging system under the electric ship’s horizontal and vertical misalignment conditions.