This paper investigates the hydrodynamics issues that are associated with AUVs (autonomous underwater vehicles) as they approach a cone-shaped dock, which is proposed by most AUV docking systems for the AUVs protection and simplification. However, this docking system is more sensitive to the hydrodynamic interactions between the dock and the ocean currents. The purpose is to exploit the hydrodynamic susceptibility in AUV docking with the dock and to identify a probable design for AUV control during docking. To achieve this purpose, numerical simulations of an AUV docking with a dock are conducted based on the dynamic mesh method. This paper illustrates the numerical methodology for AUV docking simulation. To increase the accuracy of the numerical simulation, turbulence models and grid-dependence problems are first studied. Then, 3D (three-dimensional) numerical simulations show the dependence of the AUV fluid forces near the dock on various velocities, accelerations, dock shapes, gliding modes, cross currents from several directions and rudder angles. The hydrodynamic behaviors of an AUV docking with a dock are obtained, which provide helpful suggestions for successful docking.