A new vertical axis-symmetrical dish-shaped autonomous underwater vehicle (AUV) with excellent maneuverability, known as the autonomous underwater hovering vehicle (AUH), is proposed. This study investigates an important working model of the AUH approaching a host ship in waves. The working model of AUH–Ship interactions deals with hydrodynamic interaction, seakeeping performance for communication, launch, and recovery near a free surface. The AUH is able to navigate and implement homing automation through acoustic positioning equipment, a depth sensor, a heading compass, and a Doppler velocity log (DVL) in the working area based on numerical analysis of AUH–Ship hydrodynamic performance in this study. The hydrodynamic-interaction performance of the AUH and ship near free surfaces is analyzed in the frequency and time domains using a potential-based surface-panel method based on a commercial computational fluid dynamics (CFD) solver (ANSYS-AQWA), i.e., a 3D panel code of seakeeping performance module in the ANSYS platform where the fluid is assumed to be irrotational, inviscid, and incompressible. The motion performance of the AUH approaching the host ship, with a dynamic positioning system in waves, is studied by estimating interactive response-amplitude operators (RAOs) of the AUH and host ship in 6-DOF that were estimated and analyzed at different wave amplitudes and frequencies. In the ship and AUH interaction simulations, the host ship is assumed to be a well-posed station keeping in waves with zero service speed. The AUH and ship interference effect is studied at different distances to appropriate recovery and launch positions for the AUH at the following sea and beam sea, i.e., wave-encounter angles 0° and 90°, respectively. In addition, the hydrodynamic interaction of the AUH and ship in yaw and roll at different AUH velocities is estimated. The AUH motion performance approaching the ship in long-crested irregular seas is analyzed in the time domain using the Pierson–Moskowitz wave spectrum model. Viscid hydrodynamic force on AUH motion in roll near a free surface was significant. A damping model was adopted to formulate the viscid effect to enhance the effectiveness of the ANSYS-AQWA inviscid potential-based solver. Numerical analysis of motion RAO of the AUH in roll with the damping effect was compared to the experimental data in wave-frequency range 0.2–1.0 Hz, resulting in the average error being reduced from 21.03% to 9.95% to verify the method’s accuracy. The proposed method conveniently and accurately predicted hydrodynamic-interaction characteristics and motion RAO for a dish-type AUH and host ship for the precise use of mounted sensors in waves. The results of these simulations can be used to analyze the homing automation and adaptive controllability to advance the AUV development and design.