Abstract: Pile-supported enclosure structures represented a critical infrastructure for offshore aquaculture, wherein their structural resilience under extreme wave loads directly governed economic viability and operational safety. The central challenge resided in the inherent conflict between ensuring complete containment of stock, which demanded non-overtopping designs, and minimizing wave-induced loads for structural economy. This study therefore aimed to bridge this gap by proposing, systematically evaluating, and validating a novel semi-overtopping design configuration. The primary objective was to quantitatively assess and compare the hydrodynamic performance, structural loads, and safety metrics of three distinct design philosophies, namely non-overtopping, semi-overtopping, and full-overtopping, to identify an optimal solution that balanced safety, functionality, and cost-effectiveness. A comprehensive and integrated numerical framework was established to achieve this objective. The methodology combined a three-dimensional potential flow solver for wave kinematics, a modified Morison equation for hydrodynamic load calculation on slender structural members, and a lumped-mass formulation coupled with a finite element method approach to simulate the dynamic response of the flexible netting system. Nonlinear soil-structure interaction for the piles was incorporated using established p-y curve models. The reliability of this numerical model was rigorously validated against a dedicated set of physical model tests. Experiments were conducted in a wave flume using a 1:20 scaled model of a pile-net enclosure. The model was subjected to both regular and extreme wave conditions, and the measured wave forces on the central pile under isolated and coupled pile-net conditions were compared with numerical predictions. The validation confirmed a high degree of accuracy, with deviations between simulated and measured forces remaining below 5%. Subsequent full-scale simulations under a 50-year return period extreme wave condition (9 m wave height) revealed decisive differences. For the pile system, the non-overtopping design resulted in extreme bending moments approximately four times greater than those in the full-overtopping design, corresponding to a critically low bending safety factor of 1.24. In contrast, the semi-overtopping design achieved a reduction of about 62% in the maximum pile bending moment compared to the non-overtopping scheme, elevating its safety factor to 3.45, a value much closer to the 6.19 observed for the full-overtopping design. Analysis of the net system showed peak tensions concentrated in the upper regions for all configurations. The maximum net tension in the non-overtopping design was 4.43 kN, which was 30.9% higher than the 3.38 kN in the full-overtopping design and yielded a tensile safety factor below 1.0 (0.89), indicating high rupture risk. The semi-overtopping design exhibited a maximum tension of 3.62 kN, only 6.9% higher than the full-overtopping benchmark, with a safe tensile safety factor of 1.12. Furthermore, the spatial distribution of high-stress zones differed: failure risk was localized at net-pile connections for the non-overtopping design, while it extended to net-superstructure joints for the semi- and full-overtopping designs. Therefore, the semi-overtopping design was demonstrated to be the optimal engineering compromise. It successfully mediated the core design conflict by dramatically reducing the extreme loads on the primary pile support system, thereby enhancing structural safety and potential cost savings, while maintaining net tension levels and safety factors nearly equivalent to the safest (full-overtopping) configuration, thus preserving essential anti-escape functionality. This study provided a validated, quantitative framework for the performance-based design of offshore aquaculture enclosures, directly addressing a significant gap in design theory and offering practical guidance for engineering applications in severe marine environments.