This research conducts a comprehensive numerical investigation into the hydrodynamic behavior of an Autonomous Underwater Vehicle working under the influence of surface waves at different submergence depths (S/D). Results reveal that increasing S/D from 4 to 16 reduces drag and lift coefficients by 10.12% and 20.97%, respectively, due to improved flow symmetry and reduced pressure gradients. The moment coefficient also decreases by 6.23%, enhancing vehicle stability. These findings underscore the critical role of submergence depth in minimizing wave-induced effects, improving efficiency, and optimizing AUV design and operational strategies in dynamic marine environments.