To address the practical requirements for enhancing the prediction methods of submarine maneuverability and seakeeping performance under complex sea conditions, overset mesh and sliding mesh techniques were employed to simulate the six-degree-of-freedom (6-DOF) coupled motion of the submarine, independent deflection of X-stern control surfaces, and rotation of the propeller. By integrating the Volume of Fluid (VOF) method to capture the free surface, a numerical simulation methodology for near-surface maneuvering motion of the free-running submarine model was developed. Through systematic investigations on the near-surface turning maneuvers of an X-rudder submarine under varying submergence depths in calm water and in regular waves of different wavelengths, critical challenges were resolved, including hydrodynamic coupling modeling of the hull-propeller-rudder system and the free surface, PD (Proportional-differential) control of the X-type autopilot, and PI (Proportional-integral) control of propeller rotational speed. The results demonstrated that when the submarine maneuvered excessively close to the free surface, the turning diameter, lateral advance, and maximum longitudinal advance of the X-rudder submarine increased drastically. This was primarily attributed to a significant degradation in rudder effectiveness, with secondary contributions from increased lateral forces on the propeller. Under specific wavelengths, vertical-plane motion attitude variations in the fourth quadrant during turning maneuvers induced substantial fluctuations in the normal force of the X-rudder, leading to pronounced adjustments in the drift angle and significant deviations in turning trajectories. These findings provide critical technical support for the prediction and evaluation of submarine maneuverability and seakeeping performance, as well as for the refinement of free-running submarine model experiments.