Aiming toward a better understanding of the limitations of submarine maneuverability in complex marine environments, systematic investigations of near-surface maneuvers of a generic submarine in waves were conducted. By using the sliding grid for propeller rotation and the overset grid for control plane deflection, numerical simulations of the free running submarine model under different near-surface maneuver conditions were performed. The fifth-order Stokes wave was utilized to model the regular wave. Simulated results of near-surface self-propulsion and turn maneuvers with different wavelengths, wave heights, and submergence depths were analyzed. The results demonstrated that in near-surface turn maneuvers in waves, to balance the dramatic fluctuation of the submarine's attitude, a significant dynamic deflection of rudders with the maximum angle probably reaching the upper limit was observed. The resultant effectiveness of rudders varied greatly, which directly led to a significant difference in the trajectories. The research can provide more comprehensive guidance for the prediction and evaluation of submarine maneuverability and seaworthiness.